############################################################################## # # # NOTE: This version of the mmCIF Dictionary is a draft being considered # # for approval by the IUCr Committee for the Maintenance of the CIF # # Standard. It is being released to the general community for comment # # and criticism. Production software should not rely on any # # features within this draft being available in the future. # # # # The review process is being administered through a discussion on a # # the mmCIF List Server being run out of Rutgers University. # # # # To subscribe to the mmCIF List Server, send a one line message # # containing the text: # # # # subscribe mmciflist Your Name # # # # to the email address: # # # # requests@ndbserver.rutgers.edu # # # # To post to the list, send messages to the email address: # # # # mmciflist@ndbserver.rutgers.edu # # # # Please use the list server for all questions, comments, and # # corrections that you may have concerning the draft dictionary. # # # # Should you have a question that you do not feel is appropriate # # for posting to the list, please feel free to contact the Chair # # of the IUCr Working Group on mmCIF, Paula Fitzgerald, # # Merck Research Laboratories, P.O. Box 2000, Ry50-105, # # Rahway, New Jersey, 07065 USA (paula_fitzgerald@merck.com). # # # # Questions concerning the process of review and approval of the # # mmCIF dictionary by the International Union of Crystallography # # should be addressed to the Coordinating Secretary of the IUCr # # Committee for the Maintenance of the CIF Standard, Brian McMahon, # # IUCr, 5 Abbey Square, Chester CH1 2HU, England (bm@iucr.ac.uk). # # # ############################################################################## # # # Macromolecular CIF Dictionary # # # # Paula Fitzgerald, Helen Berman, Phil Bourne, Brian McMahon, # # Keith Watenpaugh, John Westbrook # # # # Version of 1997-01-23 # # # ############################################################################## # # # This dictionary is compliant with DDL v2.1. As such, it looks # # substantially different from the previously approved and released # # versions of the CIF core dictionary. This dictionary contains all # # data items that were present in the CIF core dictionary. To those # # data items have been added the large number of data items needed to # # describe the macromolecular crystallographic experiment and its # # results. # # # ############################################################################## # # # Resources for understanding this dictionary and the mmCIF data # # structure: # # # # Data Description Language (DDL) v2.1: # # http://ndbserver.rutgers.edu/DDL # # mmCIF Dictionary: # # http://ndbserver.rutgers.edu/mmcif # # mmCIF tutorial: # # http:// # # example files: # # http://ndbserver.rutgers.edu/mmcif # # # ############################################################################## # # # For some data items, a standard syntax is assumed. The syntax is # # described for each data item in the dictionary, but is summarized here: # # # # Names: The family name(s) followed by a comma, precedes the first # # name(s) or initial(s). # # # # Telephone numbers: # # The international code is given in brackets and any extension # # number is preceded by 'ext'. # # # # Dates: In the form yyyy-mm-dd. # # # ############################################################################## data_cifdic.m97 _dictionary.title cifdic.m97 _dictionary.version 0.8.10 _dictionary.datablock_id cifdic.m97 ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with references to a Cartesian (orthogonal Angstrom) coordinate system. ; 'cartesian_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with references to a Cartesian (orthogonal Angstrom) coordinate system. ; 'fractional_coordinate' ; The collection of x, y, and z components of a position specified with references to unit cell directions. ; 'fractional_coordinate_esd' ; The collection of estimated standard deviations of the x, y, and z components of a position specified with references to unit cell directions. ; 'matrix' ; The collection of elements of a matrix. ; miller_index ; The collection of h, k, and l components of a the Miller index of a reflection. ; 'cell_length' ; The collection of a, b, and c axis lengths of a unit cell. ; 'cell_length_esd' ; The collection of estimated standard deviations of the a, b, and c axis lengths of a unit cell. ; 'cell_angle' ; The collection of alpha, beta, and gamma angles of a unit cell. ; 'cell_angle_esd' ; The collection of estimated standard deviations of the alpha, beta, and gamma angles of a unit cell. ; 'mm_atom_site_auth_label' ; The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. ; 'vector' ; The collection of elements of a vector. ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description 'inclusive_group' . ; Categories that belong to the macromolecular dictionary. ; 'atom_group' 'inclusive_group' ; Categories that describe the properties of atoms. ; 'audit_group' 'inclusive_group' ; Categories that describe dictionary maintenance and identification. ; 'cell_group' 'inclusive_group' ; Categories that describe the unit cell. ; 'chemical_group' 'inclusive_group' ; Categories that describe chemical properties and nomenclature. ; 'chem_comp_group' 'inclusive_group' ; Categories that describe components of chemical structure. ; 'chem_link_group' 'inclusive_group' ; Categories that describe linkages between components of chemical structure. ; 'citation_group' 'inclusive_group' ; Categories that provide bibliographic references. ; 'computing_group' 'inclusive_group' ; Categories that describe the computational details of the experiment. ; 'compliance_group' 'inclusive_group' ; Categories that are included in this dictionary specifically to comply with previous dictionaries. ; 'database_group' 'inclusive_group' ; Categories that hold references to other databases with related information. ; 'diffrn_group' 'inclusive_group' ; Categories that describe details of the diffraction experiment. ; 'entity_group' 'inclusive_group' ; Categories that describe chemical entities. ; 'entry_group' 'inclusive_group' ; Categories that pertain to the entire data block. ; 'exptl_group' 'inclusive_group' ; Categories which hold details of the experimental conditions. ; 'geom_group' 'inclusive_group' ; Categories which hold internal coordinates. ; 'iucr_group' 'inclusive_group' ; Categories which are used for internal processing and manuscript submission by the International Union of Crystallography staff. ; 'pdb_group' 'inclusive_group' ; Categories which pertain to the file format or data processing codes used by the Brookhaven Protein Data Bank. ; 'phasing_group' 'inclusive_group' ; Categories that describe phasing. ; 'refine_group' 'inclusive_group' ; Categories that describe refinement. ; 'refln_group' 'inclusive_group' ; Categories that describe the details of reflection measurements. ; 'struct_group' 'inclusive_group' ; Categories that contain details about the crystallographic structure. ; 'symmetry_group' 'inclusive_group' ; Categories that describe symmetry information. ; ############### ## ATOM_SITE ## ############### save_ATOM_SITE _category.description ; Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions, and so on. The data items for describing anisotropic temperature or thermal displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. ; _category.id atom_site _category.mandatory_code no _category_key.name '_atom_site.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_site.group_PDB _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.footnote_id _atom_site.auth_seq_id _atom_site.id ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 11 1 ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 11 2 ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 11 3 ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 11 4 ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 11 5 ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 11 6 ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 11 7 ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 12 8 ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 12 9 ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 12 10 ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 12 11 ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 12 12 ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 12 13 ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 12 14 ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 12 15 ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 12 16 ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 13 17 ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 13 18 ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 13 19 ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 13 20 ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 13 21 ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 13 22 ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 13 23 # - - - - data truncated for brevity - - - - HETATM C C1 APS C . 1 4.171 29.012 7.116 0.58 17.27 1 300 101 HETATM C C2 APS C . 1 4.949 27.758 6.793 0.58 16.95 1 300 102 HETATM O O3 APS C . 1 4.800 26.678 7.393 0.58 16.85 1 300 103 HETATM N N4 APS C . 1 5.930 27.841 5.869 0.58 16.43 1 300 104 # - - - - data truncated for brevity - - - - ; save_ save__atom_site.aniso_B[1][1] _item_description.description ; The [1][1] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][1]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][1]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[1][1]. ; _item.name '_atom_site.aniso_B[1][1]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2] _item_description.description ; The [1][2] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][2]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][2]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[1][2]. ; _item.name '_atom_site.aniso_B[1][2]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3] _item_description.description ; The [1][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[1][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[1][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[1][3]. ; _item.name '_atom_site.aniso_B[1][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2] _item_description.description ; The [2][2] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][2]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][2]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[2][2]. ; _item.name '_atom_site.aniso_B[2][2]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3] _item_description.description ; The [2][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[2][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[2][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[2][3]. ; _item.name '_atom_site.aniso_B[2][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3] _item_description.description ; The [3][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.aniso_B[3][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_B[3][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_B[3][3]. ; _item.name '_atom_site.aniso_B[3][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.aniso_ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site.aniso_ratio' _item.category_id atom_site _item.mandatory_code no _item_related.related_name '_atom_site_anisotrop.ratio' _item_related.function_code alternate_exclusive loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__atom_site.aniso_U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][1]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][1]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[1][1]. ; _item.name '_atom_site.aniso_U[1][1]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][2]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][2]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[1][2]. ; _item.name '_atom_site.aniso_U[1][2]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[1][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[1][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[1][3]. ; _item.name '_atom_site.aniso_U[1][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][2]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][2]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[2][2]. ; _item.name '_atom_site.aniso_U[2][2]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[2][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[2][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[2][3]. ; _item.name '_atom_site.aniso_U[2][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site.aniso_U[3][3]' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.aniso_U[3][3]_esd _item_description.description ; The estimated standard deviation of _atom_site.aniso_U[3][3]. ; _item.name '_atom_site.aniso_U[3][3]_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.aniso_U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.attached_hydrogens _item_description.description ; The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given. ; _item.name '_atom_site.attached_hydrogens' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_attached_hydrogens' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 4 4 4 0 0 0 _item_type.code int loop_ _item_examples.case _item_examples.detail 2 'water oxygen' 1 'hydroxyl oxygen' 4 'ammonium nitrogen' save_ save__atom_site.auth_asym_id _item_description.description ; An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_asym_id' atom_site no '_geom_angle.atom_site_auth_asym_id_1' geom_angle no '_geom_angle.atom_site_auth_asym_id_2' geom_angle no '_geom_angle.atom_site_auth_asym_id_3' geom_angle no '_geom_bond.atom_site_auth_asym_id_1' geom_bond no '_geom_bond.atom_site_auth_asym_id_2' geom_bond no '_geom_contact.atom_site_auth_asym_id_1' geom_contact no '_geom_contact.atom_site_auth_asym_id_2' geom_contact no '_geom_hbond.atom_site_auth_asym_id_A' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_D' geom_hbond no '_geom_hbond.atom_site_auth_asym_id_H' geom_hbond no '_geom_torsion.atom_site_auth_asym_id_1' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_2' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_3' geom_torsion no '_geom_torsion.atom_site_auth_asym_id_4' geom_torsion no '_struct_conf.beg_auth_asym_id' struct_conf no '_struct_conf.end_auth_asym_id' struct_conf no '_struct_conn.ptnr1_auth_asym_id' struct_conn no '_struct_conn.ptnr2_auth_asym_id' struct_conn no '_struct_mon_nucl.auth_asym_id' struct_mon_nucl no '_struct_mon_prot.auth_asym_id' struct_mon_prot no '_struct_mon_prot_cis.auth_asym_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_asym_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_asym_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_asym_id' struct_sheet_range no '_struct_sheet_range.end_auth_asym_id' struct_sheet_range no '_struct_site_gen.auth_asym_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_angle.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_bond.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_contact.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_A' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_D' '_atom_site.auth_asym_id' '_geom_hbond.atom_site_auth_asym_id_H' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id' '_geom_torsion.atom_site_auth_asym_id_4' '_atom_site.auth_asym_id' '_struct_conf.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conf.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr1_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conn.ptnr2_auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_nucl.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot.auth_asym_id' '_atom_site.auth_asym_id' '_struct_mon_prot_cis.auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_ncs_dom_lim.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_sheet_range.end_auth_asym_id' '_atom_site.auth_asym_id' '_struct_site_gen.auth_asym_id' '_atom_site.auth_asym_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_atom_id _item_description.description ; An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_atom_id' atom_site no '_geom_angle.atom_site_auth_atom_id_1' geom_angle no '_geom_angle.atom_site_auth_atom_id_2' geom_angle no '_geom_angle.atom_site_auth_atom_id_3' geom_angle no '_geom_bond.atom_site_auth_atom_id_1' geom_bond no '_geom_bond.atom_site_auth_atom_id_2' geom_bond no '_geom_contact.atom_site_auth_atom_id_1' geom_contact no '_geom_contact.atom_site_auth_atom_id_2' geom_contact no '_geom_hbond.atom_site_auth_atom_id_A' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_D' geom_hbond no '_geom_hbond.atom_site_auth_atom_id_H' geom_hbond no '_geom_torsion.atom_site_auth_atom_id_1' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_2' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_3' geom_torsion no '_geom_torsion.atom_site_auth_atom_id_4' geom_torsion no '_struct_conn.ptnr1_auth_atom_id' struct_conn no '_struct_conn.ptnr2_auth_atom_id' struct_conn no '_struct_sheet_hbond.range_1_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_atom_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_atom_id' struct_sheet_hbond no '_struct_site_gen.auth_atom_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_angle.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_bond.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_contact.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_A' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_D' '_atom_site.auth_atom_id' '_geom_hbond.atom_site_auth_atom_id_H' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id' '_geom_torsion.atom_site_auth_atom_id_4' '_atom_site.auth_atom_id' '_struct_conn.ptnr1_auth_atom_id' '_atom_site.auth_atom_id' '_struct_conn.ptnr2_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_1_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_beg_auth_atom_id' '_atom_site.auth_atom_id' '_struct_sheet_hbond.range_2_end_auth_atom_id' '_atom_site.auth_atom_id' '_struct_site_gen.auth_atom_id' '_atom_site.auth_atom_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_comp_id _item_description.description ; An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_comp_id' atom_site no '_geom_angle.atom_site_auth_comp_id_1' geom_angle no '_geom_angle.atom_site_auth_comp_id_2' geom_angle no '_geom_angle.atom_site_auth_comp_id_3' geom_angle no '_geom_bond.atom_site_auth_comp_id_1' geom_bond no '_geom_bond.atom_site_auth_comp_id_2' geom_bond no '_geom_contact.atom_site_auth_comp_id_1' geom_contact no '_geom_contact.atom_site_auth_comp_id_2' geom_contact no '_geom_hbond.atom_site_auth_comp_id_A' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_D' geom_hbond no '_geom_hbond.atom_site_auth_comp_id_H' geom_hbond no '_geom_torsion.atom_site_auth_comp_id_1' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_2' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_3' geom_torsion no '_geom_torsion.atom_site_auth_comp_id_4' geom_torsion no '_struct_conf.beg_auth_comp_id' struct_conf no '_struct_conf.end_auth_comp_id' struct_conf no '_struct_conn.ptnr1_auth_comp_id' struct_conn no '_struct_conn.ptnr2_auth_comp_id' struct_conn no '_struct_mon_nucl.auth_comp_id' struct_mon_nucl no '_struct_mon_prot.auth_comp_id' struct_mon_prot no '_struct_mon_prot_cis.auth_comp_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_comp_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_comp_id' struct_ncs_dom_lim no '_struct_sheet_range.beg_auth_comp_id' struct_sheet_range no '_struct_sheet_range.end_auth_comp_id' struct_sheet_range no '_struct_site_gen.auth_comp_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_angle.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_bond.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_contact.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_A' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_D' '_atom_site.auth_comp_id' '_geom_hbond.atom_site_auth_comp_id_H' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id' '_geom_torsion.atom_site_auth_comp_id_4' '_atom_site.auth_comp_id' '_struct_conf.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conf.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr1_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conn.ptnr2_auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_nucl.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot.auth_comp_id' '_atom_site.auth_comp_id' '_struct_mon_prot_cis.auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_ncs_dom_lim.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_sheet_range.end_auth_comp_id' '_atom_site.auth_comp_id' '_struct_site_gen.auth_comp_id' '_atom_site.auth_comp_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_seq_id _item_description.description ; An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any way they choose. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may to used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_seq_id' atom_site no '_geom_angle.atom_site_auth_seq_id_1' geom_angle no '_geom_angle.atom_site_auth_seq_id_2' geom_angle no '_geom_angle.atom_site_auth_seq_id_3' geom_angle no '_geom_bond.atom_site_auth_seq_id_1' geom_bond no '_geom_bond.atom_site_auth_seq_id_2' geom_bond no '_geom_contact.atom_site_auth_seq_id_1' geom_contact no '_geom_contact.atom_site_auth_seq_id_2' geom_contact no '_geom_hbond.atom_site_auth_seq_id_A' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_D' geom_hbond no '_geom_hbond.atom_site_auth_seq_id_H' geom_hbond no '_geom_torsion.atom_site_auth_seq_id_1' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_2' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_3' geom_torsion no '_geom_torsion.atom_site_auth_seq_id_4' geom_torsion no '_struct_conf.beg_auth_seq_id' struct_conf no '_struct_conf.end_auth_seq_id' struct_conf no '_struct_conn.ptnr1_auth_seq_id' struct_conn no '_struct_conn.ptnr2_auth_seq_id' struct_conn no '_struct_mon_nucl.auth_seq_id' struct_mon_nucl no '_struct_mon_prot.auth_seq_id' struct_mon_prot no '_struct_mon_prot_cis.auth_seq_id' struct_mon_prot_cis no '_struct_ncs_dom_lim.beg_auth_seq_id' struct_ncs_dom_lim no '_struct_ncs_dom_lim.end_auth_seq_id' struct_ncs_dom_lim no '_struct_sheet_hbond.range_1_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_1_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_beg_auth_seq_id' struct_sheet_hbond no '_struct_sheet_hbond.range_2_end_auth_seq_id' struct_sheet_hbond no '_struct_sheet_range.beg_auth_seq_id' struct_sheet_range no '_struct_sheet_range.end_auth_seq_id' struct_sheet_range no '_struct_site_gen.auth_seq_id' struct_site_gen no loop_ _item_linked.child_name _item_linked.parent_name '_geom_angle.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_angle.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_bond.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_contact.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_A' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_D' '_atom_site.auth_seq_id' '_geom_hbond.atom_site_auth_seq_id_H' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id' '_geom_torsion.atom_site_auth_seq_id_4' '_atom_site.auth_seq_id' '_struct_conf.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conf.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr1_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conn.ptnr2_auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_nucl.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot.auth_seq_id' '_atom_site.auth_seq_id' '_struct_mon_prot_cis.auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_ncs_dom_lim.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_1_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_hbond.range_2_end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_sheet_range.end_auth_seq_id' '_atom_site.auth_seq_id' '_struct_site_gen.auth_seq_id' '_atom_site.auth_seq_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.B_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, B~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~equiv~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalised B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_equiv_geom_mean' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean_esd' associated_esd '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_equiv_geom_mean_esd _item_description.description ; The estimated standard deviation of _atom_site.B_equiv_geom_mean. ; _item.name '_atom_site.B_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_equiv_geom_mean' associated_value '_atom_site.U_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv _item_description.description ; Isotropic temperature factor parameter, or equivalent isotropic temperature factor, B~equiv~, calculated from anisotropic temperature factor parameters. B~equiv~ = (1/3) sum~i~[sum~j~(B~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B~ij~ = 8 pi^2^ U~ij~ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site.B_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_iso_or_equiv' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv_esd' associated_esd '_atom_site.U_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.B_iso_or_equiv_esd _item_description.description ; The estimated standard deviation of _atom_site.B_iso_or_equiv. ; _item.name '_atom_site.B_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.B_iso_or_equiv' associated_value '_atom_site.U_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site.calc_attached_atom _item_description.description ; The _atom_site.id of the atom site to which the 'geometry- calculated' atom site is attached. ; _item.name '_atom_site.calc_attached_atom' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_attached_atom' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code code save_ save__atom_site.calc_flag _item_description.description ; A standard code to signal if the site data have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy coordinates. The abbreviation 'c' may be used in place of 'calc'. ; _item.name '_atom_site.calc_flag' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_calc_flag' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value d _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail d 'determined from experimental measurements' calc 'calculated from molecular geometry' c 'abbreviation for "calc"' dum 'dummy site with meaningless coordinates' save_ save__atom_site.Cartn_x _item_description.description ; The x atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_x' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_x_esd _item_description.description ; The estimated standard deviation of _atom_site.Cartn_x. ; _item.name '_atom_site.Cartn_x_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_y _item_description.description ; The y atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_y' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_z' _item_related.related_name '_atom_site.Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_y_esd _item_description.description ; The estimated standard deviation of _atom_site.Cartn_y. ; _item.name '_atom_site.Cartn_y_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_z_esd' _item_related.related_name '_atom_site.Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.Cartn_z _item_description.description ; The z atom site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_z' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_y' _item_related.related_name '_atom_site.Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_z_esd _item_description.description ; The estimated standard deviation of _atom_site.Cartn_z. ; _item.name '_atom_site.Cartn_z_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x_esd' '_atom_site.Cartn_y_esd' _item_related.related_name '_atom_site.Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__atom_site.chemical_conn_number _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_atom_site.chemical_conn_number' _item.mandatory_code no _item_aliases.alias_name '_atom_site_chemical_conn_number' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__atom_site.constraints _item_description.description ; A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints. ; _item.name '_atom_site.constraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_constraints' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case 'pop=1.0-pop(Zn3)' save_ save__atom_site.details _item_description.description ; A description of special aspects of this site. See also _atom_site.refinement_flags. ; _item.name '_atom_site.details' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_description' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'Ag/Si disordered' save_ save__atom_site.disorder_assembly _item_description.description ; A code which identifies a cluster of atoms that show long range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_assembly' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_assembly' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code code save_ save__atom_site.disorder_group _item_description.description ; A code that identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the H atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. "-1") is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_site.disorder_group' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_disorder_group' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value '.' _item_type.code code save_ save__atom_site.footnote_id _item_description.description ; The value of _atom_site.footnote_id must match an id specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list. ; _item.name '_atom_site.footnote_id' _item.mandatory_code no save_ save__atom_site.fract_x _item_description.description ; The x coordinate of the atom site position specified as a fraction of _cell.length_a. ; _item.name '_atom_site.fract_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_x' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_x_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_x_esd _item_description.description ; The estimated standard deviation of _atom_site.fract_x. ; _item.name '_atom_site.fract_x_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_y_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_x' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_y _item_description.description ; The y coordinate of the atom site position specified as a fraction of _cell.length_b. ; _item.name '_atom_site.fract_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_y' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_z' _item_related.related_name '_atom_site.fract_y_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_y_esd _item_description.description ; The estimated standard deviation of _atom_site.fract_y. ; _item.name '_atom_site.fract_y_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_z_esd' _item_related.related_name '_atom_site.fract_y' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.fract_z _item_description.description ; The z coordinate of the atom site position specified as a fraction of _cell.length_c. ; _item.name '_atom_site.fract_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_fract_z' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x' '_atom_site.fract_y' _item_related.related_name '_atom_site.fract_z_esd' _item_related.function_code associated_esd _item_sub_category.id fractional_coordinate _item_type.code float _item_type_conditions.code esd save_ save__atom_site.fract_z_esd _item_description.description ; The estimated standard deviation of _atom_site.fract_z. ; _item.name '_atom_site.fract_z_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_atom_site.fract_x_esd' '_atom_site.fract_y_esd' _item_related.related_name '_atom_site.fract_z' _item_related.function_code associated_value _item_sub_category.id fractional_coordinate_esd _item_type.code float save_ save__atom_site.group_PDB _item_description.description ; The group of atoms to which the _atom_site. belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_atom_site.group_PDB' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value ATOM HETATM save_ save__atom_site.id _item_description.description ; The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to facilitate compatibility between small molecule and macromolecular files. In the small molecule files, _atom_site_label is the identifier for the atom. In the macromolecular files, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying atoms. For compatibility with older files, _atom_site_label is aliased to _atom_site.id. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.id' atom_site yes '_atom_site_anisotrop.id' atom_site_anisotrop yes '_geom_angle.atom_site_id_1' geom_angle yes '_geom_angle.atom_site_id_2' geom_angle yes '_geom_angle.atom_site_id_3' geom_angle yes '_geom_bond.atom_site_id_1' geom_bond yes '_geom_bond.atom_site_id_2' geom_bond yes '_geom_contact.atom_site_id_1' geom_contact yes '_geom_contact.atom_site_id_2' geom_contact yes '_geom_hbond.atom_site_id_A' geom_hbond yes '_geom_hbond.atom_site_id_D' geom_hbond yes '_geom_hbond.atom_site_id_H' geom_hbond yes '_geom_torsion.atom_site_id_1' geom_torsion yes '_geom_torsion.atom_site_id_2' geom_torsion yes '_geom_torsion.atom_site_id_3' geom_torsion yes '_geom_torsion.atom_site_id_4' geom_torsion yes _item_aliases.alias_name '_atom_site_label' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site_anisotrop.id' '_atom_site.id' '_geom_angle.atom_site_id_1' '_atom_site.id' '_geom_angle.atom_site_id_2' '_atom_site.id' '_geom_angle.atom_site_id_3' '_atom_site.id' '_geom_bond.atom_site_id_1' '_atom_site.id' '_geom_bond.atom_site_id_2' '_atom_site.id' '_geom_contact.atom_site_id_1' '_atom_site.id' '_geom_contact.atom_site_id_2' '_atom_site.id' '_geom_hbond.atom_site_id_A' '_atom_site.id' '_geom_hbond.atom_site_id_D' '_atom_site.id' '_geom_hbond.atom_site_id_H' '_atom_site.id' '_geom_torsion.atom_site_id_1' '_atom_site.id' '_geom_torsion.atom_site_id_2' '_atom_site.id' '_geom_torsion.atom_site_id_3' '_atom_site.id' '_geom_torsion.atom_site_id_4' '_atom_site.id' _item_type.code code loop_ _item_examples.case '5' 'C12' 'Ca3g28' 'Fe3+17' 'H*251' 'boron2a' 'C_a_phe_83_a_0' 'Zn_Zn_301_A_0' save_ save__atom_site.label_alt_id _item_description.description ; A component of the macromolecular identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_site.label_alt_id' _item.mandatory_code no _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_asym_id _item_description.description ; A component of the macromolecular identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_atom_site.label_asym_id' _item.mandatory_code no _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_atom_id _item_description.description ; A component of the macromolecular identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_atom_site.label_atom_id' _item.mandatory_code no _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_comp_id _item_description.description ; A component of the macromolecular identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_atom_site.label_comp_id' _item.mandatory_code no _item_sub_category.id mm_atom_site_label save_ save__atom_site.label_entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_atom_site.label_entity_id' _item.mandatory_code no save_ save__atom_site.label_seq_id _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_atom_site.label_seq_id' _item.mandatory_code no save_ save__atom_site.occupancy _item_description.description ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. ; _item.name '_atom_site.occupancy' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_occupancy' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 1.0 loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_related.related_name '_atom_site.occupancy_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd save_ save__atom_site.occupancy_esd _item_description.description ; The estimated standard deviation of _atom_site.occupancy. ; _item.name '_atom_site.occupancy_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_atom_site.occupancy' _item_related.function_code associated_value _item_type.code float save_ save__atom_site.refinement_flags _item_description.description ; A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. ; _item.name '_atom_site.refinement_flags' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_refinement_flags' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail . 'no refinement constraints' S 'special position constraint on site' G 'rigid group refinement of site' R 'riding atom site attached to non-riding atom' D 'distance or angle restraint on site' T 'thermal displacement constraints' U 'Uiso or Uij restraint (rigid bond)' P 'partial occupancy constraint' save_ save__atom_site.restraints _item_description.description ; A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints. ; _item.name '_atom_site.restraints' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_restraints' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'restrained to planar ring' save_ save__atom_site.symmetry_multiplicity _item_description.description ; The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography, Vol. A (1987). ; _item.name '_atom_site.symmetry_multiplicity' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_symmetry_multiplicity' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 192 192 192 1 1 1 _item_type.code int save_ save__atom_site.thermal_displace_type _item_description.description ; A standard code used to describe the type of atomic displacement parameters used for the site. ; _item.name '_atom_site.thermal_displace_type' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_thermal_displace_type' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail Uani 'anisotropic Uij' Uiso 'isotropic U' Uovl 'overall U' Umpe 'multipole expansion U' Bani 'anisotropic Bij' Biso 'isotropic B' Bovl 'overall B' save_ save__atom_site.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_type_symbol' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__atom_site.U_equiv_geom_mean _item_description.description ; Equivalent isotropic atomic displacement parameter, U~equiv~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~equiv~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalised U~ij~ ; _item.name '_atom_site.U_equiv_geom_mean' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_equiv_geom_mean' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean_esd' associated_esd '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_equiv_geom_mean_esd _item_description.description ; The estimated standard deviation of _atom_site.U_equiv_geom_mean. ; _item.name '_atom_site.U_equiv_geom_mean_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_equiv_geom_mean' associated_value '_atom_site.B_equiv_geom_mean' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~equiv~, calculated from anisotropic atomic displacement parameters. U~equiv~ = (1/3) sum~i~[sum~j~(U~ij~ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. ; _item.name '_atom_site.U_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_U_iso_or_equiv' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 10.0 10.0 10.0 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv_esd' associated_esd '_atom_site.B_iso_or_equiv' conversion_constant _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site.U_iso_or_equiv_esd _item_description.description ; The estimated standard deviation of _atom_site.U_iso_or_equiv. ; _item.name '_atom_site.U_iso_or_equiv_esd' _item.category_id atom_site _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site.U_iso_or_equiv' associated_value '_atom_site.B_iso_or_equiv_esd' conversion_constant _item_type.code float _item_units.code angstroms_squared save_ save__atom_site.Wyckoff_symbol _item_description.description ; The Wyckoff symbol (letter) as listed in the space-group section of International Tables for Crystallography, Vol. A (1987). ; _item.name '_atom_site.Wyckoff_symbol' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Wyckoff_symbol' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ ######################### ## ATOM_SITE_ANISOTROP ## ######################### save_ATOM_SITE_ANISOTROP _category.description ; Data items in the ATOM_SITE_ANISOTROP category record details about temperature or thermal displacement factors, if those data items are contained in a separate list from the ATOM_SITE list. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. ; _category.id atom_site_anisotrop _category.mandatory_code no _category_key.name '_atom_site_anisotrop.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_site_anisotrop.B[1][1] _item_description.description ; The [1][1] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_11' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]_esd' associated_esd '_atom_site.aniso_U[1][1]' conversion_constant '_atom_site_anisotrop.U[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.U[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][1]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[1][1]. ; _item.name '_atom_site_anisotrop.B[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][1]' associated_value '_atom_site.aniso_U[1][1]_esd' conversion_constant '_atom_site_anisotrop.U[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2] _item_description.description ; The [1][2] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_12' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]_esd' associated_esd '_atom_site.aniso_U[1][2]' conversion_constant '_atom_site_anisotrop.U[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.U[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][2]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[1][2]. ; _item.name '_atom_site_anisotrop.B[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][2]' associated_value '_atom_site.aniso_U[1][2]_esd' conversion_constant '_atom_site_anisotrop.U[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3] _item_description.description ; The [1][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_13' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]_esd' associated_esd '_atom_site.aniso_U[1][3]' conversion_constant '_atom_site_anisotrop.U[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.U[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[1][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[1][3]. ; _item.name '_atom_site_anisotrop.B[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[1][3]' associated_value '_atom_site.aniso_U[1][3]_esd' conversion_constant '_atom_site_anisotrop.U[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2] _item_description.description ; The [2][2] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_22' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]_esd' associated_esd '_atom_site.aniso_U[2][2]' conversion_constant '_atom_site_anisotrop.U[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.U[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][2]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[2][2]. ; _item.name '_atom_site_anisotrop.B[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][2]' associated_value '_atom_site.aniso_U[2][2]_esd' conversion_constant '_atom_site_anisotrop.U[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3] _item_description.description ; The [2][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_23' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]_esd' associated_esd '_atom_site.aniso_U[2][3]' conversion_constant '_atom_site_anisotrop.U[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.U[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[2][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[2][3]. ; _item.name '_atom_site_anisotrop.B[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[2][3]' associated_value '_atom_site.aniso_U[2][3]_esd' conversion_constant '_atom_site_anisotrop.U[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3] _item_description.description ; The [3][3] element of the anisotropic thermal displacement matrix B, which appears in the structure factor term as: T = exp{-1/4 sum~i~[sum~j~(B~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. ; _item.name '_atom_site_anisotrop.B[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_B_33' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]_esd' associated_esd '_atom_site.aniso_U[3][3]' conversion_constant '_atom_site_anisotrop.U[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.U[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.B[3][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.B[3][3]. ; _item.name '_atom_site_anisotrop.B[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.B[3][3]' associated_value '_atom_site.aniso_U[3][3]_esd' conversion_constant '_atom_site_anisotrop.U[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.U[3][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code 8pi2_angstroms_squared save_ save__atom_site_anisotrop.ratio _item_description.description ; Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. ; _item.name '_atom_site_anisotrop.ratio' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_ratio' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_related.related_name '_atom_site.aniso_ratio' _item_related.function_code alternate_exclusive _item_type.code float save_ save__atom_site_anisotrop.id _item_description.description ; This data item is a pointer to _atom_site.id in the ATOM_SITE category. ; _item.name '_atom_site_anisotrop.id' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_label' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__atom_site_anisotrop.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site_anisotrop.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_atom_site_aniso_type_symbol' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__atom_site_anisotrop.U[1][1] _item_description.description ; The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][1]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_11' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]_esd' associated_esd '_atom_site.aniso_B[1][1]' conversion_constant '_atom_site_anisotrop.B[1][1]' conversion_constant '_atom_site.aniso_B[1][1]' alternate_exclusive '_atom_site.aniso_U[1][1]' alternate_exclusive '_atom_site_anisotrop.B[1][1]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][1]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[1][1]. ; _item.name '_atom_site_anisotrop.U[1][1]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][1]' associated_value '_atom_site.aniso_B[1][1]_esd' conversion_constant '_atom_site_anisotrop.B[1][1]_esd' conversion_constant '_atom_site.aniso_B[1][1]_esd' alternate_exclusive '_atom_site.aniso_U[1][1]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][1]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2] _item_description.description ; The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_12' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]_esd' associated_esd '_atom_site.aniso_B[1][2]' conversion_constant '_atom_site_anisotrop.B[1][2]' conversion_constant '_atom_site.aniso_B[1][2]' alternate_exclusive '_atom_site.aniso_U[1][2]' alternate_exclusive '_atom_site_anisotrop.B[1][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][2]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[1][2]. ; _item.name '_atom_site_anisotrop.U[1][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][2]' associated_value '_atom_site.aniso_B[1][2]_esd' conversion_constant '_atom_site_anisotrop.B[1][2]_esd' conversion_constant '_atom_site.aniso_B[1][2]_esd' alternate_exclusive '_atom_site.aniso_U[1][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3] _item_description.description ; The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[1][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_13' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]_esd' associated_esd '_atom_site.aniso_B[1][3]' conversion_constant '_atom_site_anisotrop.B[1][3]' conversion_constant '_atom_site.aniso_B[1][3]' alternate_exclusive '_atom_site.aniso_U[1][3]' alternate_exclusive '_atom_site_anisotrop.B[1][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[1][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[1][3]. ; _item.name '_atom_site_anisotrop.U[1][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[1][3]' associated_value '_atom_site.aniso_B[1][3]_esd' conversion_constant '_atom_site_anisotrop.B[1][3]_esd' conversion_constant '_atom_site.aniso_B[1][3]_esd' alternate_exclusive '_atom_site.aniso_U[1][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[1][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2] _item_description.description ; The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][2]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_22' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]_esd' associated_esd '_atom_site.aniso_B[2][2]' conversion_constant '_atom_site_anisotrop.B[2][2]' conversion_constant '_atom_site.aniso_B[2][2]' alternate_exclusive '_atom_site.aniso_U[2][2]' alternate_exclusive '_atom_site_anisotrop.B[2][2]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][2]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[2][2]. ; _item.name '_atom_site_anisotrop.U[2][2]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][2]' associated_value '_atom_site.aniso_B[2][2]_esd' conversion_constant '_atom_site_anisotrop.B[2][2]_esd' conversion_constant '_atom_site.aniso_B[2][2]_esd' alternate_exclusive '_atom_site.aniso_U[2][2]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][2]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3] _item_description.description ; The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[2][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_23' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]_esd' associated_esd '_atom_site.aniso_B[2][3]' conversion_constant '_atom_site_anisotrop.B[2][3]' conversion_constant '_atom_site.aniso_B[2][3]' alternate_exclusive '_atom_site.aniso_U[2][3]' alternate_exclusive '_atom_site_anisotrop.B[2][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[2][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[2][3]. ; _item.name '_atom_site_anisotrop.U[2][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[2][3]' associated_value '_atom_site.aniso_B[2][3]_esd' conversion_constant '_atom_site_anisotrop.B[2][3]_esd' conversion_constant '_atom_site.aniso_B[2][3]_esd' alternate_exclusive '_atom_site.aniso_U[2][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[2][3]_esd' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3] _item_description.description ; The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure factor term: T = exp{-2 pi^2^ sum~i~[sum~j~(U~ij~ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. ; _item.name '_atom_site_anisotrop.U[3][3]' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_aliases.alias_name '_atom_site_aniso_U_33' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]_esd' associated_esd '_atom_site.aniso_B[3][3]' conversion_constant '_atom_site_anisotrop.B[3][3]' conversion_constant '_atom_site.aniso_B[3][3]' alternate_exclusive '_atom_site.aniso_U[3][3]' alternate_exclusive '_atom_site_anisotrop.B[3][3]' alternate_exclusive _item_sub_category.id matrix _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_squared save_ save__atom_site_anisotrop.U[3][3]_esd _item_description.description ; The estimated standard deviation of _atom_site_anisotrop.U[3][3]. ; _item.name '_atom_site_anisotrop.U[3][3]_esd' _item.category_id atom_site_anisotrop _item.mandatory_code no _item_default.value 0.0 loop_ _item_related.related_name _item_related.function_code '_atom_site_anisotrop.U[3][3]' associated_value '_atom_site.aniso_B[3][3]_esd' conversion_constant '_atom_site_anisotrop.B[3][3]_esd' conversion_constant '_atom_site.aniso_B[3][3]_esd' alternate_exclusive '_atom_site.aniso_U[3][3]_esd' alternate_exclusive '_atom_site_anisotrop.B[3][3]_esd' alternate_exclusive _item_type.code float _item_units.code angstroms_squared save_ ################ ## ATOM_SITES ## ################ save_ATOM_SITES _category.description ; Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. ; _category.id atom_sites _category.mandatory_code no _category_key.name '_atom_sites.entry_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP ; ; _atom_sites.entry_id '5HVP' _atom_sites.Cartn_transform_axes 'c along z, astar along x, b along y' _atom_sites.Cartn_transf_matrix[1][1] 58.39 _atom_sites.Cartn_transf_matrix[1][2] 0.00 _atom_sites.Cartn_transf_matrix[1][3] 0.00 _atom_sites.Cartn_transf_matrix[2][1] 0.00 _atom_sites.Cartn_transf_matrix[2][2] 86.70 _atom_sites.Cartn_transf_matrix[2][3] 0.00 _atom_sites.Cartn_transf_matrix[3][1] 0.00 _atom_sites.Cartn_transf_matrix[3][2] 0.00 _atom_sites.Cartn_transf_matrix[3][3] 46.27 _atom_sites.Cartn_transf_vector[1] 0.00 _atom_sites.Cartn_transf_vector[2] 0.00 _atom_sites.Cartn_transf_vector[3] 0.00 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_atom_sites.entry_id' _item.mandatory_code yes save_ save__atom_sites.Cartn_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_11' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_12' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_13' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_21' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][2] _item_description.description ; The [2][2] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_22' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_23' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_31' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_32' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_33' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.Cartn_transf_vector[1] _item_description.description ; The [1] element of the 3 element vector and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_1' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[2] _item_description.description ; The [2] element of the 3 element vector and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_2' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transf_vector[3] _item_description.description ; The [3] element of the 3 element vector and used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.Cartn_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_tran_vector_3' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.Cartn_transform_axes _item_description.description ; A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix. ; _item.name '_atom_sites.Cartn_transform_axes' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_Cartn_transform_axes' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'a parallel to x; b in the plane of y & z' save_ save__atom_sites.fract_transf_matrix[1][1] _item_description.description ; The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_11' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][2] _item_description.description ; The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_12' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[1][3] _item_description.description ; The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[1][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_13' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][1] _item_description.description ; The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_21' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][2] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_22' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[2][3] _item_description.description ; The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[2][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_23' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][1] _item_description.description ; The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_31' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][2] _item_description.description ; The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_32' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_matrix[3][3] _item_description.description ; The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_matrix[3][3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_matrix_33' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_sub_category.id matrix _item_type.code float save_ save__atom_sites.fract_transf_vector[1] _item_description.description ; The [1] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[1]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_1' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[2] _item_description.description ; The [2] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[2]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_2' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.fract_transf_vector[3] _item_description.description ; The [3] element of the 3 element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| ; _item.name '_atom_sites.fract_transf_vector[3]' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_fract_tran_vector_3' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__atom_sites.solution_primary _item_description.description ; A code which identifies the methods used to locate the initial atomic sites. The solution_primary code identifies how the first atom sites were determined. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_primary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_primary' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_secondary _item_description.description ; A code which identifies the methods used to locate the initial atomic sites. The solution_secondary code identifies how the non-hydrogen sites not include in solution_primary were located. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_secondary' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_secondary' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ save__atom_sites.solution_hydrogens _item_description.description ; A code which identifies the methods used to locate the initial atomic sites. The solution_hydrogens code identifies how the hydrogens were located. *** This data item would not in general be used in a macromolecular data block. *** ; _item.name '_atom_sites.solution_hydrogens' _item.category_id atom_sites _item.mandatory_code no _item_aliases.alias_name '_atom_sites_solution_hydrogens' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail difmap 'difference Fourier map' vecmap 'real-space vector search' heavy 'heavy-atom method' direct 'structure-invariant direct methods' geom 'inferred from neighbouring sites' disper 'anomalous-dispersion techniques' isomor 'isomorphous structure methods' save_ #################### ## ATOM_SITES_ALT ## #################### save_ATOM_SITES_ALT _category.description ; Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modeled in alternative conformations in this data block. ; _category.id atom_sites_alt _category.mandatory_code no _category_key.name '_atom_sites_alt.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt.id _atom_sites_alt.details '.' ; Atom sites with the alternative id set to null are not modeled in alternative conformations ; '1' ; Atom sites with the alternative id set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative id 2. The conformations of amino acid side chains and solvent atoms with alternative id set to 1 correlate with the conformation of the inhibitor marked with alternative id 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor. ; '2' ; Atom sites with the alternative id set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative id 1. The conformations of amino acid side chains and solvent atoms with alternative id set to 2 correlate with the conformation of the inhibitor marked with alternative id 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor. ; '3' ; Atom sites with the alternative id set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative id 4. The conformations of amino acid side chains and solvent atoms with alternative id set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; '4' ; Atom sites with the alternative id set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative id 3. The conformations of amino acid side chains and solvent atoms with alternative id set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt.details _item_description.description ; A description of special aspects of the modeling of atoms in alternative conformations. ; _item.name '_atom_sites_alt.details' _item.category_id atom_sites_alt _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt.id _item_description.description ; The value of _atom_sites_alt.id must uniquely identify a record in the _atom_sites_alt. list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt.id' atom_sites_alt yes '_atom_site.label_alt_id' atom_site no '_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes '_geom_angle.atom_site_label_alt_id_1' geom_angle no '_geom_angle.atom_site_label_alt_id_2' geom_angle no '_geom_angle.atom_site_label_alt_id_3' geom_angle no '_geom_bond.atom_site_label_alt_id_1' geom_bond no '_geom_bond.atom_site_label_alt_id_2' geom_bond no '_geom_contact.atom_site_label_alt_id_1' geom_contact no '_geom_contact.atom_site_label_alt_id_2' geom_contact no '_geom_hbond.atom_site_label_alt_id_A' geom_hbond no '_geom_hbond.atom_site_label_alt_id_D' geom_hbond no '_geom_hbond.atom_site_label_alt_id_H' geom_hbond no '_geom_torsion.atom_site_label_alt_id_1' geom_torsion no '_geom_torsion.atom_site_label_alt_id_2' geom_torsion no '_geom_torsion.atom_site_label_alt_id_3' geom_torsion no '_geom_torsion.atom_site_label_alt_id_4' geom_torsion no '_struct_conn.ptnr1_label_alt_id' struct_conn no '_struct_conn.ptnr2_label_alt_id' struct_conn no '_struct_mon_nucl.label_alt_id' struct_mon_nucl yes '_struct_mon_prot.label_alt_id' struct_mon_prot yes '_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_alt_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_alt_id' struct_ncs_dom_lim yes '_struct_site_gen.label_alt_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_alt_id' '_atom_sites_alt.id' '_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id' '_geom_angle.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_angle.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_bond.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_contact.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_A' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_D' '_atom_site.label_alt_id' '_geom_hbond.atom_site_label_alt_id_H' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_1' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_2' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_3' '_atom_site.label_alt_id' '_geom_torsion.atom_site_label_alt_id_4' '_atom_site.label_alt_id' '_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id' '_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id' '_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id' '_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.beg_label_alt_id' '_atom_site.label_alt_id' '_struct_ncs_dom_lim.end_label_alt_id' '_atom_site.label_alt_id' '_struct_site_gen.label_alt_id' '_atom_site.label_alt_id' _item_type.code code loop_ _item_examples.case 'orientation 1' 'molecule abc' save_ ######################## ## ATOM_SITES_ALT_ENS ## ######################## save_ATOM_SITES_ALT_ENS _category.description ; Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation ids. ; _category.id atom_sites_alt_ens _category.mandatory_code no _category_key.name '_atom_sites_alt_ens.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt_ens.id _atom_sites_alt_ens.details 'Ensemble 1-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric, alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 1-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (id=1) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-A' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; 'Ensemble 2-B' ; The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (id=2) and the amino acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (id=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_ens.details _item_description.description ; A description of special aspects of the ensemble structure generated from atoms with various alternative ids. ; _item.name '_atom_sites_alt_ens.details' _item.category_id atom_sites_alt_ens _item.mandatory_code no _item_type.code text save_ save__atom_sites_alt_ens.id _item_description.description ; The value of _atom_sites_alt_ens.id must uniquely identify a record in the _atom_sites_alt_ens. list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_alt_ens.id' atom_sites_alt_ens yes '_atom_sites_alt_gen.ens_id' atom_sites_alt_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_ens.id' _item_type.code code save_ ######################## ## ATOM_SITES_ALT_GEN ## ######################## save_ATOM_SITES_ALT_GEN _category.description ; Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. ; _category.id atom_sites_alt_gen _category.mandatory_code no loop_ _category_key.name '_atom_sites_alt_gen.ens_id' '_atom_sites_alt_gen.alt_id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_alt_gen.ens_id _atom_sites_alt_gen.alt_id 'Ensemble 1-A' '.' 'Ensemble 1-A' '1' 'Ensemble 1-A' '3' 'Ensemble 1-B' '.' 'Ensemble 1-B' '1' 'Ensemble 1-B' '4' 'Ensemble 2-A' '.' 'Ensemble 2-A' '2' 'Ensemble 2-A' '3' 'Ensemble 2-B' '.' 'Ensemble 2-B' '2' 'Ensemble 2-B' '4' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_alt_gen.alt_id _item_description.description ; This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category. ; _item.name '_atom_sites_alt_gen.alt_id' _item.mandatory_code yes save_ save__atom_sites_alt_gen.ens_id _item_description.description ; This data item is a pointer to _atom_sites_alt_ens.id in the ATOM_SITES_ALT_ENS category. ; _item.name '_atom_sites_alt_gen.ens_id' _item.mandatory_code yes save_ ######################### ## ATOM_SITES_FOOTNOTE ## ######################### save_ATOM_SITES_FOOTNOTE _category.description ; Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or group of atom sites. ; _category.id atom_sites_footnote _category.mandatory_code no _category_key.name '_atom_sites_footnote.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_sites_footnote.id _atom_sites_footnote.text 1 ; The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative ids *1* and *2*. ; 2 ; Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 3 ; The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative id *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative id *2* and occupancy 0.42 correlate with inhibitor orientation *2*. ; 4 ; Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor. ; 5 ; The positions of these water molecules correlate with alternative orientations of amino acid side chains that do not correlate with alternative orientations of the inhibitor. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_sites_footnote.id _item_description.description ; A code that identifies the footnote. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_sites_footnote.id' atom_sites_footnote yes '_atom_site.footnote_id' atom_site no loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.footnote_id' '_atom_sites_footnote.id' _item_type.code code loop_ _item_examples.case 'a' 'b' '1' '2' save_ save__atom_sites_footnote.text _item_description.description ; The text of the footnote. Footnotes are used to describe an atom site or group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modeled, among many other possibilities. ; _item.name '_atom_sites_footnote.text' _item.category_id atom_sites_footnote _item.mandatory_code no _item_type.code text save_ ############### ## ATOM_TYPE ## ############### save_ATOM_TYPE _category.description ; Data items in the ATOM_TYPE category record details about properties of the atoms that occupy the atom sites, such as the atomic scattering factors. ; _category.id atom_type _category.mandatory_code no _category_key.name '_atom_type.symbol' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c C 0 2.31000 20.8439 1.02000 10.2075 1.58860 0.568700 0.865000 51.6512 0.21560 N 0 12.2126 0.005700 3.13220 9.89330 2.01250 28.9975 1.16630 0.582600 -11.529 O 0 3.04850 13.2771 2.28680 5.70110 1.54630 0.323900 0.867000 32.9089 0.250800 S 0 6.90530 1.46790 5.20340 22.2151 1.43790 0.253600 1.58630 56.1720 0.866900 CL -1 18.2915 0.006600 7.20840 1.17170 6.53370 19.5424 2.33860 60.4486 -16.378 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; loop_ _atom_type.symbol _atom_type.oxidation_number _atom_type.number_in_cell _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_source C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_type.analytical_mass_percent _item_description.description ; Mass percentage of this atom type derived from chemical analysis. ; _item.name '_atom_type.analytical_mass_percent' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_analytical_mass_%' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float save_ save__atom_type.description _item_description.description ; A description of the atom(s) designated by this atom type. In most cases this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. ; _item.name '_atom_type.description' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_description' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'deuterium' '0.34Fe+0.66Ni' save_ save__atom_type.number_in_cell _item_description.description ; Total number of atoms of this atom type in the unit cell. ; _item.name '_atom_type.number_in_cell' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_number_in_cell' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__atom_type.oxidation_number _item_description.description ; Formal oxidation state of this atom type in the structure. ; _item.name '_atom_type.oxidation_number' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_oxidation_number' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 6 6 6 -6 -6 -6 _item_type.code int save_ save__atom_type.radius_bond _item_description.description ; The effective intramolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_bond' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_bond' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 4.0 4.0 4.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.radius_contact _item_description.description ; The effective intermolecular bonding radius in angstroms of this atom type. ; _item.name '_atom_type.radius_contact' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_radius_contact' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 4.0 4.0 4.0 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ save__atom_type.scat_Cromer_Mann_a1 _item_description.description ; The a1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a2 _item_description.description ; The a2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a3 _item_description.description ; The a3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_a4 _item_description.description ; The a4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_a4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b1 _item_description.description ; The b1 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b1' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b2 _item_description.description ; The b2 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b2' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b3 _item_description.description ; The b3 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b3' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b4' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_b4 _item_description.description ; The b4 Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_b4' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_c' _item_type.code float save_ save__atom_type.scat_Cromer_Mann_c _item_description.description ; The c Cromer-Mann scattering-factor coefficient used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography, Vol. IV, (1974). Table 2.2B. or: International Tables for Crystallography, Vol. C, (1991). Tables 6.1.1.4 and 6.1.1.5. ; _item.name '_atom_type.scat_Cromer_Mann_c' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_atom_type.scat_Cromer_Mann_a1' '_atom_type.scat_Cromer_Mann_a2' '_atom_type.scat_Cromer_Mann_a3' '_atom_type.scat_Cromer_Mann_a4' '_atom_type.scat_Cromer_Mann_b1' '_atom_type.scat_Cromer_Mann_b2' '_atom_type.scat_Cromer_Mann_b3' '_atom_type.scat_Cromer_Mann_b4' _item_type.code float save_ save__atom_type.scat_dispersion_imag _item_description.description ; The imaginary component of the anomalous dispersion scattering factors, f'' (in electrons) for this atom type and the radiation given in _diffrn_radiation.wavelength. ; _item.name '_atom_type.scat_dispersion_imag' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_imag' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_real' _item_type.code float save_ save__atom_type.scat_dispersion_real _item_description.description ; The real component of the anomalous dispersion scattering factors, and f' (in electrons) for this atom type and the radiation given in _diffrn_radiation.wavelength. ; _item.name '_atom_type.scat_dispersion_real' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_dispersion_real' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0.0 _item_dependent.dependent_name '_atom_type.scat_dispersion_imag' _item_type.code float save_ save__atom_type.scat_length_neutron _item_description.description ; The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. ; _item.name '_atom_type.scat_length_neutron' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_length_neutron' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_units.code femtometres save_ save__atom_type.scat_source _item_description.description ; Reference to source of scattering factors used for this atom type. ; _item.name '_atom_type.scat_source' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_source' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'International Tables Vol IV Table 2.4.6B' save_ save__atom_type.scat_versus_stol_list _item_description.description ; A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. ; _item.name '_atom_type.scat_versus_stol_list' _item.category_id atom_type _item.mandatory_code no _item_aliases.alias_name '_atom_type_scat_versus_stol_list' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__atom_type.symbol _item_description.description ; The code used to identify the atom specie(s) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underline with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes '_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes '_chemical_conn_atom.type_symbol' chemical_conn_atom yes '_chem_comp_atom.type_symbol' chem_comp_atom yes '_phasing_MIR_der_site.atom_type_symbol' phasing_MIR_der_site yes _item_aliases.alias_name '_atom_type_symbol' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.type_symbol' '_atom_type.symbol' '_atom_site_anisotrop.type_symbol' '_atom_type.symbol' '_chemical_conn_atom.type_symbol' '_atom_type.symbol' '_chem_comp_atom.type_symbol' '_atom_type.symbol' '_phasing_MIR_der_site.atom_type_symbol' '_atom_type.symbol' _item_type.code code loop_ _item_examples.case 'C' 'Cu2+' 'H(SDS)' 'dummy' 'FeNi' save_ ########### ## AUDIT ## ########### save_AUDIT _category.description ; Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items (in the JOURNAL category) that describe the time course of publication of the material in the data block. ; _category.id audit _category.mandatory_code no _category_key.name '_audit.revision_id' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _audit.revision_id 1 _audit.creation_date '1992-12-08' _audit.creation_method ; Created by hand from PDB entry 5HVP, from the JBC paper describing this structure and from laboratory records ; _audit.update_record ; 1992-12-09 adjusted to reflect comments from Brian McKeever 1992-12-10 adjusted to reflect comments from Helen Berman 1992-12-12 adjusted to reflect comments from Keith Watenpaugh ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _audit.creation_date 1991-03-20 _audit.creation_method from_xtal_archive_file_using_CIFIO _audit.update_record ; 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec'd by co-editor with diagram as manuscript HL7. 1991-04-17 adjustments based on first referees report. 1991-04-18 adjustments based on second referees report. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit.creation_date _item_description.description ; A date that the data block was created. The date format is yyyy-mm-dd. ; _item.name '_audit.creation_date' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_date' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code yyyy-mm-dd _item_examples.case '1990-07-12' save_ save__audit.creation_method _item_description.description ; A description of how data were entered into the data block. ; _item.name '_audit.creation_method' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_creation_method' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'spawned by the program QBEE' save_ save__audit.revision_id _item_description.description ; The value of _audit.revision_id must uniquely identify a record in the AUDIT list. ; _item.name '_audit.revision_id' _item.category_id audit _item.mandatory_code yes _item_type.code code _item_examples.case 'rev1' save_ save__audit.update_record _item_description.description ; A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. ; _item.name '_audit.update_record' _item.category_id audit _item.mandatory_code no _item_aliases.alias_name '_audit_update_record' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case '1990-07-15 Updated by the Co-editor' save_ ################## ## AUDIT_AUTHOR ## ################## save_AUDIT_AUTHOR _category.description ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. ; _category.id audit_author _category.mandatory_code no _category_key.name '_audit_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _audit_author.name _audit_author.address 'Fitzgerald, Paula M.D.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'McKeever, Brian M.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Van Middlesworth, J.F.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; 'Springer, James P.' ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_author.address _item_description.description ; The address of an author of this data block. If there are multiple authors, _audit_author.address is looped with _audit_author.name. ; _item.name '_audit_author.address' _item.category_id audit_author _item.mandatory_code no _item_aliases.alias_name '_audit_author_address' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_author.name _item_description.description ; The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). ; _item.name '_audit_author.name' _item.category_id audit_author _item.mandatory_code yes _item_aliases.alias_name '_audit_author_name' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ ################### ## AUDIT_CONFORM ## ################### save_AUDIT_CONFORM _category.description ; Data items in the AUDIT_CONFORM category described the dictionary versions against which the data names appearing in the current data block are conformant. ; _category.id audit_conform _category.mandatory_code no loop_ _category_key.name '_audit_conform.dict_name' '_audit_conform.dict_version' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Any file conforming to the current CIF core dictionary. ; ; _audit_conform.dict_name cif_core.dic _audit_conform.dict_version 2.0 _audit_conform.dict_location ftp://ftp.iucr.ac.uk/pub/cifdic.c96 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_conform.dict_location _item_description.description ; A file name or uniform resource locator (URL) where the conformant dictionary resides. ; _item.name '_audit_conform.dict_location' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_location' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__audit_conform.dict_name _item_description.description ; The string identifying the highest-level dictionary defining datanames used in this file. ; _item.name '_audit_conform.dict_name' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_name' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__audit_conform.dict_version _item_description.description ; The version number of the conformant dictionary. ; _item.name '_audit_conform.dict_version' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_version' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ ########################## ## AUDIT_CONTACT_AUTHOR ## ########################## save_AUDIT_CONTACT_AUTHOR _category.description ; Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. ; _category.id audit_contact_author _category.mandatory_code no _category_key.name '_audit_contact_author.name' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _audit_contact_author.name 'Fitzgerald, Paula M.D.' _audit_contact_author.address ; Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA ; _audit_contact_author.phone '908 594 5510' _audit_contact_author.fax '908 594 6645' _audit_contact_author.email 'paula_fitzgerald@merck.com' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_contact_author.address _item_description.description ; The mailing address of the author of the data block to whom correspondence should be addressed. ; _item.name '_audit_contact_author.address' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_address' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; Department Institute Street City and postcode COUNTRY ; save_ save__audit_contact_author.email _item_description.description ; The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognisable to international networks. ; _item.name '_audit_contact_author.email' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_email' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'name@host.domain.country' 'bm@iucr.ac.uk' save_ save__audit_contact_author.fax _item_description.description ; The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. ; _item.name '_audit_contact_author.fax' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_fax' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case '12(34)9477334' '12()349477334' save_ save__audit_contact_author.name _item_description.description ; The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_contact_author.name' _item.category_id audit_contact_author _item.mandatory_code yes _item_aliases.alias_name '_audit_contact_author_name' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__audit_contact_author.phone _item_description.description ; The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. ; _item.name '_audit_contact_author.phone' _item.category_id audit_contact_author _item.mandatory_code no _item_aliases.alias_name '_audit_contact_author_phone' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case '12(34)9477330' '12()349477330' '12(34)9477330x5543' save_ ########## ## CELL ## ########## save_CELL _category.description ; Data items in the CELL category record details about the crystallographic cell parameters. ; _category.id cell _category.mandatory_code no _category_key.name '_cell.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _cell.entry_id '5HVP' _cell.length_a 58.39 _cell.length_a_esd 0.05 _cell.length_b 86.70 _cell.length_b_esd 0.12 _cell.length_c 46.27 _cell.length_c_esd 0.06 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.volume 234237 _cell.details ; The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _cell.length_a 5.959 _cell.length_a_esd 0.001 _cell.length_b 14.956 _cell.length_b_esd 0.001 _cell.length_c 19.737 _cell.length_c_esd 0.003 _cell.angle_alpha 90.0 _cell.angle_beta 90.0 _cell.angle_gamma 90.0 _cell.volume 1759.0 _cell.volume_esd 0.3 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell.angle_alpha _item_description.description ; Unit-cell angle alpha in degrees of the reported structure. ; _item.name '_cell.angle_alpha' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_alpha' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_beta' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_alpha_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_alpha_esd _item_description.description ; The estimated standard deviation of _cell.angle_alpha. ; _item.name '_cell.angle_alpha_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_beta_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_alpha' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_beta _item_description.description ; Unit-cell angle beta in degrees of the reported structure. ; _item.name '_cell.angle_beta' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_beta' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_gamma' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_beta_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_beta_esd _item_description.description ; The estimated standard deviation of _cell.angle_beta. ; _item.name '_cell.angle_beta_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_gamma_esd' _item_related.related_name '_cell.angle_beta' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.angle_gamma _item_description.description ; Unit-cell angle gamma in degrees of the reported structure. ; _item.name '_cell.angle_gamma' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_angle_gamma' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 90.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha' '_cell.angle_beta' loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_cell.angle_gamma_esd' _item_related.function_code associated_esd _item_sub_category.id cell_angle _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__cell.angle_gamma_esd _item_description.description ; The estimated standard deviation of _cell.angle_gamma. ; _item.name '_cell.angle_gamma_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.angle_alpha_esd' '_cell.angle_beta_esd' _item_related.related_name '_cell.angle_gamma' _item_related.function_code associated_value _item_sub_category.id cell_angle_esd _item_type.code float _item_units.code degrees save_ save__cell.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell.entry_id' _item.mandatory_code yes save_ save__cell.details _item_description.description ; A description of special aspects of the cell choice, noting possible alternative settings. ; _item.name '_cell.details' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_special_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'pseudo-orthorhombic' ; standard setting from 45 deg rotation around c ; save_ save__cell.formula_units_Z _item_description.description ; The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum. ; _item.name '_cell.formula_units_Z' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_formula_units_Z' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__cell.length_a _item_description.description ; Unit-cell length a corresponding to the structure reported. ; _item.name '_cell.length_a' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_a' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_a_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_a_esd _item_description.description ; The estimated standard deviation of _cell.length_a. ; _item.name '_cell.length_a_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_b_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_a' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_b _item_description.description ; Unit-cell length b corresponding to the structure reported. ; _item.name '_cell.length_b' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_b' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell.length_b' '_cell.length_c' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_b_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_b_esd _item_description.description ; The estimated standard deviation of _cell.length_b. ; _item.name '_cell.length_b_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_c_esd' _item_related.related_name '_cell.length_b' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.length_c _item_description.description ; Unit-cell length c corresponding to the structure reported. ; _item.name '_cell.length_c' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_length_c' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell.length_a' '_cell.length_b' loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.length_c_esd' _item_related.function_code associated_esd _item_sub_category.id cell_length _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__cell.length_c_esd _item_description.description ; The estimated standard deviation of _cell.length_c. ; _item.name '_cell.length_c_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_cell.length_a_esd' '_cell.length_b_esd' _item_related.related_name '_cell.length_c' _item_related.function_code associated_value _item_sub_category.id cell_length_esd _item_type.code float _item_units.code angstroms save_ save__cell.volume _item_description.description ; Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = _cell.length_a b = _cell.length_b c = _cell.length_c alpha = _cell.angle_alpha beta = _cell.angle_beta gamma = _cell.angle_gamma ; _item.name '_cell.volume' _item.category_id cell _item.mandatory_code no _item_aliases.alias_name '_cell_volume' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell.volume_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__cell.volume_esd _item_description.description ; The estimated standard deviation of _cell.volume. ; _item.name '_cell.volume_esd' _item.category_id cell _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_cell.volume' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ save__cell.Z_PDB _item_description.description ; The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. This is not a very satisfactory definition, as the multiplicity of macromolecular structures can be different for the different components of the cell. A more useful measure of a "macro- molecular Z" could be obtained by counting the number of times each molecular entity appears in the STRUCT_ASYM list and multiplying by the number of equivalent positions in the unit cell. There would be one such number for each type of molecular entity. ; _item.name '_cell.Z_PDB' _item.category_id cell _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ ###################### ## CELL_MEASUREMENT ## ###################### save_CELL_MEASUREMENT _category.description ; Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. ; _category.id cell_measurement _category.mandatory_code no _category_key.name '_cell_measurement.entry_id' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _cell_measurement.entry_id '5HVP' _cell_measurement.temp 293 _cell_measurement.temp_esd 3 _cell_measurement.theta_min 11 _cell_measurement.theta_max 31 _cell_measurement.wavelength 1.54 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _cell_measurement.temp 293 _cell_measurement.reflns_used 25 _cell_measurement.theta_min 25 _cell_measurement.theta_max 31 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_cell_measurement.entry_id' _item.mandatory_code yes save_ save__cell_measurement.pressure _item_description.description ; The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure used to synthesize the sample). ; _item.name '_cell_measurement.pressure' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_pressure' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_related.related_name '_cell_measurement.pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__cell_measurement.pressure_esd _item_description.description ; The estimated standard deviation of _cell_measurement.pressure. ; _item.name '_cell_measurement.pressure_esd' _item.category_id cell_measurement _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_cell_measurement.pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__cell_measurement.radiation _item_description.description ; Description of the radiation used to measure the unit-cell data. See also _cell_measurement.wavelength. ; _item.name '_cell_measurement.radiation' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_radiation' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'neutron' 'Cu K\a' 'synchrotron' save_ save__cell_measurement.reflns_used _item_description.description ; The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. ; _item.name '_cell_measurement.reflns_used' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_reflns_used' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code int save_ save__cell_measurement.temp _item_description.description ; The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). ; _item.name '_cell_measurement.temp' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_temperature' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_cell_measurement.temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvin save_ save__cell_measurement.temp_esd _item_description.description ; The estimated standard deviation of _cell_measurement.temp. ; _item.name '_cell_measurement.temp_esd' _item.category_id cell_measurement _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_cell_measurement.temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvin save_ save__cell_measurement.theta_max _item_description.description ; The maximum theta angle in degrees of reflections used to measure the unit cell. ; _item.name '_cell_measurement.theta_max' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_max' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.theta_min _item_description.description ; The minimum theta angle in degrees of reflections used to measure the unit cell. ; _item.name '_cell_measurement.theta_min' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_theta_min' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ save__cell_measurement.wavelength _item_description.description ; The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be the same as that given in _diffrn_radiation.wavelength. ; _item.name '_cell_measurement.wavelength' _item.category_id cell_measurement _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_wavelength' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code angstroms save_ ############################ ## CELL_MEASUREMENT_REFLN ## ############################ save_CELL_MEASUREMENT_REFLN _category.description ; Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used in determination of the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. ; _category.id cell_measurement_refln _category.mandatory_code no loop_ _category_key.name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' loop_ _category_group.id 'inclusive_group' 'cell_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__cell_measurement_refln.index_h _item_description.description ; Miller index h of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_h' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_h' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_k' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_k _item_description.description ; Miller index k of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_k' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_k' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_l' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.index_l _item_description.description ; Miller index l of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.index_l' _item.category_id cell_measurement_refln _item.mandatory_code yes _item_aliases.alias_name '_cell_measurement_refln_index_l' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_dependent.dependent_name '_cell_measurement_refln.index_h' '_cell_measurement_refln.index_k' _item_sub_category.id miller_index _item_type.code int save_ save__cell_measurement_refln.theta _item_description.description ; Theta angle in degrees of a reflection used for measurement of the unit cell. ; _item.name '_cell_measurement_refln.theta' _item.category_id cell_measurement_refln _item.mandatory_code no _item_aliases.alias_name '_cell_measurement_refln_theta' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum 90.0 90.0 90.0 0.0 0.0 0.0 _item_type.code float _item_units.code degrees save_ ############### ## CHEM_COMP ## ############### save_CHEM_COMP _category.description ; Data items in the CHEM_COMP category give details (such as name, mass, charge, etc.) about each of the chemical components from which the relevant chemical structures can be constructed. The related CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE, etc. categories describe the detailed geometry of these chemical components. ; _category.id chem_comp _category.mandatory_code no _category_key.name '_chem_comp.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp.id _chem_comp.model_source _chem_comp.name phe '1987 Protin/Prolsq Ideals file' phenylalanine val '1987 Protin/Prolsq Ideals file' alanine # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp.formula _item_description.description ; The formula for the chemical component. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. ; _item.name '_chem_comp.formula' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chem_comp.formula_weight _item_description.description ; Formula mass in daltons of the chemical component. ; _item.name '_chem_comp.formula_weight' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chem_comp.id _item_description.description ; The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.id' chem_comp yes '_atom_site.label_comp_id' atom_site no '_chem_comp.mon_nstd_parent_comp_id' chem_comp no '_chem_comp_atom.comp_id' chem_comp_atom yes '_chem_comp_angle.comp_id' chem_comp_angle yes '_chem_comp_bond.comp_id' chem_comp_bond yes '_chem_comp_chir.comp_id' chem_comp_chir yes '_chem_comp_chir_atom.comp_id' chem_comp_chir_atom yes '_chem_comp_plane.comp_id' chem_comp_plane yes '_chem_comp_plane_atom.comp_id' chem_comp_plane_atom yes '_chem_comp_tor.comp_id' chem_comp_tor yes '_chem_comp_tor_value.comp_id' chem_comp_tor_value yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_geom_angle.atom_site_label_comp_id_1' geom_angle no '_geom_angle.atom_site_label_comp_id_2' geom_angle no '_geom_angle.atom_site_label_comp_id_3' geom_angle no '_geom_bond.atom_site_label_comp_id_1' geom_bond no '_geom_bond.atom_site_label_comp_id_2' geom_bond no '_geom_contact.atom_site_label_comp_id_1' geom_contact no '_geom_contact.atom_site_label_comp_id_2' geom_contact no '_geom_hbond.atom_site_label_comp_id_A' geom_hbond no '_geom_hbond.atom_site_label_comp_id_D' geom_hbond no '_geom_hbond.atom_site_label_comp_id_H' geom_hbond no '_geom_torsion.atom_site_label_comp_id_1' geom_torsion no '_geom_torsion.atom_site_label_comp_id_2' geom_torsion no '_geom_torsion.atom_site_label_comp_id_3' geom_torsion no '_geom_torsion.atom_site_label_comp_id_4' geom_torsion no '_struct_conf.beg_label_comp_id' struct_conf yes '_struct_conf.end_label_comp_id' struct_conf yes '_struct_conn.ptnr1_label_comp_id' struct_conn yes '_struct_conn.ptnr2_label_comp_id' struct_conn yes '_struct_mon_nucl.label_comp_id' struct_mon_nucl yes '_struct_mon_prot.label_comp_id' struct_mon_prot yes '_struct_mon_prot_cis.label_comp_id' struct_mon_prot_cis yes '_struct_ncs_dom_lim.beg_label_comp_id' struct_ncs_dom_lim yes '_struct_ncs_dom_lim.end_label_comp_id' struct_ncs_dom_lim yes '_struct_ref_seq_dif.db_mon_id' struct_ref_seq_dif yes '_struct_ref_seq_dif.mon_id' struct_ref_seq_dif yes '_struct_sheet_range.beg_label_comp_id' struct_sheet_range yes '_struct_sheet_range.end_label_comp_id' struct_sheet_range yes '_struct_site_gen.label_comp_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_comp_id' '_chem_comp.id' '_chem_comp.mon_nstd_parent_comp_id' '_chem_comp.id' '_chem_comp_atom.comp_id' '_chem_comp.id' '_chem_comp_chir.comp_id' '_chem_comp.id' '_chem_comp_chir_atom.comp_id' '_chem_comp.id' '_chem_comp_plane.comp_id' '_chem_comp.id' '_chem_comp_plane_atom.comp_id' '_chem_comp.id' '_entity_poly_seq.mon_id' '_chem_comp.id' '_chem_comp_angle.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_bond.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor.comp_id' '_chem_comp_atom.comp_id' '_chem_comp_tor_value.comp_id' '_chem_comp_atom.comp_id' '_geom_angle.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_angle.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_bond.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_contact.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_A' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_D' '_atom_site.label_comp_id' '_geom_hbond.atom_site_label_comp_id_H' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_1' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_2' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_3' '_atom_site.label_comp_id' '_geom_torsion.atom_site_label_comp_id_4' '_atom_site.label_comp_id' '_struct_conf.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_conf.end_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr1_label_comp_id' '_atom_site.label_comp_id' '_struct_conn.ptnr2_label_comp_id' '_atom_site.label_comp_id' '_struct_mon_nucl.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot.label_comp_id' '_atom_site.label_comp_id' '_struct_mon_prot_cis.label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_ncs_dom_lim.end_label_comp_id' '_atom_site.label_comp_id' '_struct_ref_seq_dif.db_mon_id' '_chem_comp.id' '_struct_ref_seq_dif.mon_id' '_chem_comp.id' '_struct_sheet_range.beg_label_comp_id' '_atom_site.label_comp_id' '_struct_sheet_range.end_label_comp_id' '_atom_site.label_comp_id' '_struct_site_gen.label_comp_id' '_atom_site.label_comp_id' _item_type.code ucode loop_ _item_examples.case 'ala' 'val' 'A' 'C' save_ save__chem_comp.model_details _item_description.description ; A description of special aspects of the generation of the coordinates for the model of the component. ; _item.name '_chem_comp.model_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text _item_examples.case 'geometry idealized but not minimized' save_ save__chem_comp.model_erf _item_description.description ; A pointer to an 'external reference file', if the atomic description of the component is taken from such a file. ; _item.name '_chem_comp.model_erf' _item.category_id chem_comp _item.mandatory_code no _item_type.code line save_ save__chem_comp.model_source _item_description.description ; The source of the coordinates for the model of the component. ; _item.name '_chem_comp.model_source' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'CSD entry ABCDEF' 'built using Quanta/Charmm' save_ save__chem_comp.mon_nstd_class _item_description.description ; A description of the class of a non-standard monomer, if the group represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_class' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'iodinated base' 'phosphorylated amino acid' 'bromined base' 'modified amino acid' 'glycosylated amino acid' save_ save__chem_comp.mon_nstd_details _item_description.description ; A description of special details of a non-standard monomer. ; _item.name '_chem_comp.mon_nstd_details' _item.category_id chem_comp _item.mandatory_code no _item_type.code text save_ save__chem_comp.mon_nstd_flag _item_description.description ; 'yes' indicates that this is a "standard" monomer, 'no' that it is "non-standard." Non-standard monomers should be further described using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class, and _chem_comp.mon_nstd_details data items. ; _item.name '_chem_comp.mon_nstd_flag' _item.category_id chem_comp _item.mandatory_code no _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'the monomer is non-standard' n 'abbreviation for "no"' yes 'the monomer is standard' y 'abbreviation for "yes"' save_ save__chem_comp.mon_nstd_parent _item_description.description ; A name of the parent monomer of the non-standard monomer, if this group represents a modification of a standard monomer. ; _item.name '_chem_comp.mon_nstd_parent' _item.category_id chem_comp _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'tyrosine' 'cytosine' save_ save__chem_comp.mon_nstd_parent_comp_id _item_description.description ; The identifier for the parent component of the non-standard component. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp.mon_nstd_parent_comp_id' _item.mandatory_code no save_ save__chem_comp.name _item_description.description ; The full name of the component. ; _item.name '_chem_comp.name' _item.category_id chem_comp _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine' save_ save__chem_comp.number_atoms_all _item_description.description ; The total number of atoms in the component. ; _item.name '_chem_comp.number_atoms_all' _item.category_id chem_comp _item.mandatory_code no _item_type.code int save_ save__chem_comp.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the component. ; _item.name '_chem_comp.number_atoms_nh' _item.category_id chem_comp _item.mandatory_code no _item_type.code int save_ save__chem_comp.one_letter_code _item_description.description ; For standard polymer components, the one-letter code for the component. If there is not a standard one letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.one_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar1 loop_ _item_examples.case _item_examples.detail A 'alanine or adenine' R 'arginine' N 'asparagine' D 'aspartic-acid' C 'cysteine or cystine or cytosine' Q 'glutamine' E 'glutamic-acid' G 'glycine or guanine' H 'histidine' I 'isoleucine' L 'leucine' K 'lysine' M 'methionine' F 'phenylalanine' P 'proline' S 'serine' T 'threonine or thymine' W 'tryptophan' Y 'tyrosine' V 'valine' U 'uracil' O 'water' X 'other' save_ save__chem_comp.three_letter_code _item_description.description ; For standard polymer components, the three-letter code for the component. If there is not a standard three letter code for this component, or if this is a non-polymer component, the three-letter code should be given as 'UNK'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component. ; _item.name '_chem_comp.three_letter_code' _item.category_id chem_comp _item.mandatory_code no _item_type.code uchar3 loop_ _item_examples.case _item_examples.detail ALA 'alanine' ARG 'arginine' ASN 'asparagine' ASP 'aspartic-acid' ASX 'ambiguous asparagine/aspartic-acid' CYS 'cysteine' GLN 'glutamine' GLU 'glutamic-acid' GLY 'glycine' HIS 'histidine' ILE 'isoleucine' LEU 'leucine' LYS 'lysine' MET 'methionine' PHE 'phenylalanine' PRO 'proline' SER 'serine' THR 'threonine' TRP 'tryptophan' TRY 'tyrosine' VAL 'valine' 1MA '1-methyladenosine' 5MC '5-methycytosine' OMC '2(prime)-O-methycytodine' 1MG '1-methyguanosine' 2MG 'N(2)-methyguanosine' M2G 'N(2)-dimethyguanosine' 7MG '7-methyguanosine' 0MG '2(prime)-O-methyguanosine' H2U 'diydrouridine' 5MU 'ribosylthymidine' PSU 'pseudouridine' ACE 'acetic acid' FOR 'formic acid' HOH 'water' UNK 'other' save_ save__chem_comp.type _item_description.description ; For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap, and monomers with some type of C-terminal (or 3') cap. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.type' chem_comp yes '_chem_comp_link.type_comp_1' chem_comp_link yes '_chem_comp_link.type_comp_2' chem_comp_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_link.type_comp_1' '_chem_comp.type' '_chem_comp_link.type_comp_2' '_chem_comp.type' _item_type.code uline loop_ _item_enumeration.value 'D-peptide linking' 'L-peptide linking' 'D-peptide NH3 amino terminus' 'L-peptide NH3 amino terminus' 'D-peptide COOH carboxy terminus' 'L-peptide COOH carboxy terminus' 'DNA linking' 'RNA linking' 'DNA OH 5 prime terminus' 'RNA OH 5 prime terminus' 'DNA OH 3 prime terminus' 'RNA OH 3 prime terminus' 'D-saccharide 1,4 and 1,4 linking' 'L-saccharide 1,4 and 1,4 linking' 'D-saccharide 1,4 and 1,6 linking' 'L-saccharide 1,4 and 1,6 linking' 'non-polymer' 'other' save_ ###################### ## CHEM_COMP_ANGLE ## ###################### save_CHEM_COMP_ANGLE _category.description ; Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. ; _category.id chem_comp_angle _category.mandatory_code no loop_ _category_key.name '_chem_comp_angle.comp_id' '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_dist phe N CA C xxx.xx x.xx phe CA C O xxx.xx x.xx phe CB CA C xxx.xx x.xx phe CB CA N xxx.xx x.xx phe CA CB CG xxx.xx x.xx phe CB CG CD1 xxx.xx x.xx phe CB CG CD2 xxx.xx x.xx phe CD1 CG CD2 xxx.xx x.xx phe CG CD1 CE1 xxx.xx x.xx phe CD1 CE1 CZ xxx.xx x.xx phe CE1 CZ CE2 xxx.xx x.xx phe CZ CE2 CD2 xxx.xx x.xx phe CG CD2 CE2 xxx.xx x.xx val N CA C xxx.xx x.xx val CA C O xxx.xx x.xx val CB CA C xxx.xx x.xx val CB CA N xxx.xx x.xx val CA CB CG1 xxx.xx x.xx val CA CB CG2 xxx.xx x.xx val CG1 CB CG2 xxx.xx x.xx ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_angle.atom_id_1 _item_description.description ; The id of the first of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_chem_comp_angle.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_2' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_2 _item_description.description ; The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_chem_comp_angle.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_3 _item_description.description ; The id of the third of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_chem_comp_angle.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_angle.atom_id_1' '_chem_comp_angle.atom_id_2' save_ save__chem_comp_angle.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_angle.comp_id' _item.mandatory_code yes save_ save__chem_comp_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_angle.value_angle' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_angle.value_angle_esd _item_description.description ; The estimated standard deviation of _chem_comp_angle.value_angle. ; _item.name '_chem_comp_angle.value_angle_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_comp_angle.value_dist' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_angle.value_dist_esd _item_description.description ; The estimated standard deviation of _chem_comp_angle.value_dist_esd. ; _item.name '_chem_comp_angle.value_dist_esd' _item.category_id chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ##################### ## CHEM_COMP_ATOM ## ##################### save_CHEM_COMP_ATOM _category.description ; Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Atomic coordinates can be given for the components; specifying coordinates is an alternative to specifying the structure of the component via bonds, angles, planes, etc., in the appropriate CHEM_COMP subcategories. ; _category.id chem_comp_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_atom.comp_id' '_chem_comp_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.substruct_code _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z phe N N main 1.20134 0.84658 0.00000 phe CA C main 0.00000 0.00000 0.00000 phe C C main -1.25029 0.88107 0.00000 phe O O main -2.18525 0.66029 -0.78409 phe CB C side 0.00662 -1.03603 1.11081 phe CG C side 0.03254 -0.49711 2.50951 phe CD1 C side -1.15813 -0.12084 3.13467 phe CE1 C side -1.15720 0.38038 4.42732 phe CZ C side 0.05385 0.51332 5.11032 phe CE2 C side 1.26137 0.11613 4.50975 phe CD2 C side 1.23668 -0.38351 3.20288 val N N main 1.20134 0.84658 0.00000 val CA C main 0.00000 0.00000 0.00000 val C C main -1.25029 0.88107 0.00000 val O O main -2.18525 0.66029 -0.78409 val CB C side 0.05260 -0.99339 1.17429 val CG1 C side -0.13288 -0.31545 2.52668 val CG2 C side -0.94265 -2.12930 0.99811 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_atom.alt_atom_id _item_description.description ; An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labeling atoms in a group. ; _item.name '_chem_comp_atom.alt_atom_id' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code line save_ save__chem_comp_atom.atom_id _item_description.description ; The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_atom.atom_id' chem_comp_atom yes '_atom_site.label_atom_id' atom_site no '_chem_comp_angle.atom_id_1' chem_comp_angle yes '_chem_comp_angle.atom_id_2' chem_comp_angle yes '_chem_comp_angle.atom_id_3' chem_comp_angle yes '_chem_comp_bond.atom_id_1' chem_comp_bond yes '_chem_comp_bond.atom_id_2' chem_comp_bond yes '_chem_comp_chir.atom_id' chem_comp_chir yes '_chem_comp_chir_atom.atom_id' chem_comp_chir_atom yes '_chem_comp_plane_atom.atom_id' chem_comp_plane_atom yes '_chem_comp_tor.atom_id_1' chem_comp_tor yes '_chem_comp_tor.atom_id_2' chem_comp_tor yes '_chem_comp_tor.atom_id_3' chem_comp_tor yes '_chem_comp_tor.atom_id_4' chem_comp_tor yes '_geom_angle.atom_site_label_atom_id_1' geom_angle no '_geom_angle.atom_site_label_atom_id_2' geom_angle no '_geom_angle.atom_site_label_atom_id_3' geom_angle no '_geom_bond.atom_site_label_atom_id_1' geom_bond no '_geom_bond.atom_site_label_atom_id_2' geom_bond no '_geom_contact.atom_site_label_atom_id_1' geom_contact no '_geom_contact.atom_site_label_atom_id_2' geom_contact no '_geom_hbond.atom_site_label_atom_id_A' geom_hbond no '_geom_hbond.atom_site_label_atom_id_D' geom_hbond no '_geom_hbond.atom_site_label_atom_id_H' geom_hbond no '_geom_torsion.atom_site_label_atom_id_1' geom_torsion no '_geom_torsion.atom_site_label_atom_id_2' geom_torsion no '_geom_torsion.atom_site_label_atom_id_3' geom_torsion no '_geom_torsion.atom_site_label_atom_id_4' geom_torsion no '_struct_conn.ptnr1_label_atom_id' struct_conn yes '_struct_conn.ptnr2_label_atom_id' struct_conn yes '_struct_sheet_hbond.range_1_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_1_end_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_beg_label_atom_id' struct_sheet_hbond yes '_struct_sheet_hbond.range_2_end_label_atom_id' struct_sheet_hbond yes '_struct_site_gen.label_atom_id' struct_site_gen yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_atom_id' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_angle.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_bond.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_chir.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_1' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_2' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_3' '_chem_comp_atom.atom_id' '_chem_comp_tor.atom_id_4' '_chem_comp_atom.atom_id' '_geom_angle.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_angle.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_bond.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_contact.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_A' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_D' '_atom_site.label_atom_id' '_geom_hbond.atom_site_label_atom_id_H' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_1' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_2' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_3' '_atom_site.label_atom_id' '_geom_torsion.atom_site_label_atom_id_4' '_atom_site.label_atom_id' '_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id' '_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_1_end_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_beg_label_atom_id' '_atom_site.label_atom_id' '_struct_sheet_hbond.range_2_end_label_atom_id' '_atom_site.label_atom_id' '_struct_site_gen.label_atom_id' '_atom_site.label_atom_id' _item_type.code code save_ save__chem_comp_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chem_comp_atom.charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 6 6 6 -6 -6 -6 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chem_comp_atom.model_Cartn_x _item_description.description ; The x component of the coordinates for this atom in this component specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. ; _item.name '_chem_comp_atom.model_Cartn_x' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_x_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_x_esd _item_description.description ; The estimated standard deviation of _chem_comp_atom.model_Cartn_x. ; _item.name '_chem_comp_atom.model_Cartn_x_esd' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_y_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_x' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y _item_description.description ; The y component of the coordinates for this atom in this component specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. ; _item.name '_chem_comp_atom.model_Cartn_y' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_z' _item_related.related_name '_chem_comp_atom.model_Cartn_y_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_y_esd _item_description.description ; The estimated standard deviation of _chem_comp_atom.model_Cartn_y. ; _item.name '_chem_comp_atom.model_Cartn_y_esd' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_z_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_y' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z _item_description.description ; The x component of the coordinates for this atom in this component specified as orthogonal Angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, and not to atom sites in the _atom_site list. ; _item.name '_chem_comp_atom.model_Cartn_z' _item.category_id chem_comp_atom _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x' '_chem_comp_atom.model_Cartn_y' _item_related.related_name '_chem_comp_atom.model_Cartn_z_esd' _item_related.function_code associated_esd _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_atom.model_Cartn_z_esd _item_description.description ; The estimated standard deviation of _chem_comp_atom.model_Cartn_z. ; _item.name '_chem_comp_atom.model_Cartn_z_esd' _item.category_id chem_comp_atom _item.mandatory_code no _item_default.value 0.0 loop_ _item_dependent.dependent_name '_chem_comp_atom.model_Cartn_x_esd' '_chem_comp_atom.model_Cartn_y_esd' _item_related.related_name '_chem_comp_atom.model_Cartn_z' _item_related.function_code associated_value _item_sub_category.id cartesian_coordinate_esd _item_type.code float _item_units.code angstroms save_ save__chem_comp_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_atom.partial_charge _item_description.description ; The partial charge assigned to this atom. ; _item.name '_chem_comp_atom.partial_charge' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code float save_ save__chem_comp_atom.substruct_code _item_description.description ; This data item assigns the atom to a substructure of the component, if appropriate. ; _item.name '_chem_comp_atom.substruct_code' _item.category_id chem_comp_atom _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail main 'main chain of an amino acid' side 'side chain of an amino acid' base 'base of a nucleic acid' phos 'phosphate of a nucleic acid' sugar 'sugar of a nucleic acid' none 'not appropriate for this monomer' save_ #save_chem_comp_atom.type_energy # _item_description.description #; This data item is a pointer to _atom_type_energy.type in the # ATOM_TYPE_ENERGY category. #; # save_ save__chem_comp_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chem_comp_atom.type_symbol' _item.mandatory_code yes save_ ##################### ## CHEM_COMP_BOND ## ##################### save_CHEM_COMP_BOND _category.description ; Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. ; _category.id chem_comp_bond _category.mandatory_code no loop_ _category_key.name '_chem_comp_bond.comp_id' '_chem_comp_bond.atom_id_1' '_chem_comp_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.value_dist phe N CA sing x.xx phe CA C sing x.xx phe C O doub x.xx phe CB CA sing x.xx phe CB CG sing x.xx phe CG CD1 arom x.xx phe CD1 CE1 arom x.xx phe CE1 CZ arom x.xx phe CZ CE2 arom x.xx phe CE2 CD2 arom x.xx phe CD2 CG arom x.xx val N CA sing x.xx val CA C sing x.xx val C O doub x.xx val CB CA sing x.xx val CB CG1 sing x.xx val CB CG2 sing x.xx ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_bond.atom_id_1 _item_description.description ; The id of the first of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_1' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_2' save_ save__chem_comp_bond.atom_id_2 _item_description.description ; The id of the second of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_bond.atom_id_2' _item.mandatory_code yes _item_dependent.dependent_name '_chem_comp_bond.atom_id_1' save_ save__chem_comp_bond.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_bond.comp_id' _item.mandatory_code yes save_ save__chem_comp_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_comp_bond.value_order' _item.category_id chem_comp_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalised double bond' pi 'pi bond' save_ save__chem_comp_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_comp_bond.value_dist' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_bond.value_dist_esd _item_description.description ; The estimated standard deviation of _chem_comp_bond.value_dist. ; _item.name '_chem_comp_bond.value_dist_esd' _item.category_id chem_comp_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_CHIR ## #################### save_CHEM_COMP_CHIR _category.description ; Data items in the CHEM_COMP_CHIR category provide detail about the chiral centers in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. ; _category.id chem_comp_chir _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir.comp_id' '_chem_comp_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id phe phe1 CA val val1 CA # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir.atom_id _item_description.description ; The id of the atom that is a chiral center. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral center. ; _item.name '_chem_comp_chir.atom_config' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_comp_chir.id _item_description.description ; The value of _chem_comp_chir.id must uniquely identify a record in the CHEM_COMP_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_chir.id' chem_comp_chir yes '_chem_comp_chir_atom.chir_id' chem_comp_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir.id' _item_type.code code save_ save__chem_comp_chir.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_all' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_comp_chir.atom_id. ; _item.name '_chem_comp_chir.number_atoms_nh' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code int save_ save__chem_comp_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_comp_chir.volume_flag' _item.category_id chem_comp_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_comp_chir.volume_three _item_description.description ; The chiral volume V(c), for chiral centers that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_comp_chir.volume_three' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_comp_chir.volume_three_esd _item_description.description ; The estimated standard deviation of _chem_comp_chir.volume_three. ; _item.name '_chem_comp_chir.volume_three_esd' _item.category_id chem_comp_chir _item.mandatory_code no _item_related.related_name '_chem_comp_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_COMP_CHIR_ATOM ## ######################### save_CHEM_COMP_CHIR_ATOM _category.description ; Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. ; _category.id chem_comp_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_chir_atom.chir_id' '_chem_comp_chir_atom.atom_id' '_chem_comp_chir_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_chir_atom.comp_id _chem_comp_chir_atom.chir_id _chem_comp_chir_atom.atom_id phe 1 N phe 1 C phe 1 CB val 1 N val 1 C val 1 CB # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_chir_atom.atom_id _item_description.description ; The id of an atom bonded to the chiral atom. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_chir_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_comp_chir.id in the CHEM_COMP_CHIR category. ; _item.name '_chem_comp_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_chir_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_chir_atom.dev _item_description.description ; The estimated standard deviation of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_comp_chir_atom.dev' _item.category_id chem_comp_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_COMP_LINK ## #################### save_CHEM_COMP_LINK _category.description ; Data items in the CHEM_COMP_LINK category give details about the linkages between chemical components. ; _category.id chem_comp_link _category.mandatory_code no _category_key.name '_chem_comp_link.link_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_link.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_comp_link.link_id' _item.mandatory_code yes save_ save__chem_comp_link.details _item_description.description ; A description of special aspects of a linkage between chemical components in the structure. ; _item.name '_chem_comp_link.details' _item.category_id chem_comp_link _item.mandatory_code no _item_type.code text save_ save__chem_comp_link.type_comp_1 _item_description.description ; The type of the first of the two components joined by the linkage. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_1' _item.mandatory_code yes save_ save__chem_comp_link.type_comp_2 _item_description.description ; The type of the second of the two components joined by the linkage. This data item is a pointer to _chem_comp.type in the CHEM_COMP category. ; _item.name '_chem_comp_link.type_comp_2' _item.mandatory_code yes save_ ###################### ## CHEM_COMP_PLANE ## ###################### save_CHEM_COMP_PLANE _category.description ; Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. ; _category.id chem_comp_plane _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane.comp_id' '_chem_comp_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_plane.comp_id _chem_comp_plane.id phe phe1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane.id _item_description.description ; The value of _chem_comp_plane.id must uniquely identify a record in the CHEM_COMP_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_plane.id' chem_comp_plane yes '_chem_comp_plane_atom.plane_id' chem_comp_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane.id' _item_type.code code save_ save__chem_comp_plane.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_all' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ save__chem_comp_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_comp_plane.number_atoms_nh' _item.category_id chem_comp_plane _item.mandatory_code no _item_type.code int save_ ########################### ## CHEM_COMP_PLANE_ATOM ## ########################### save_CHEM_COMP_PLANE_ATOM _category.description ; Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. ; _category.id chem_comp_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_comp_plane_atom.plane_id' '_chem_comp_plane_atom.atom_id' '_chem_comp_plane_atom.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.atom_id phe1 phe CB phe1 phe CG phe1 phe CD1 phe1 phe CE1 phe1 phe CZ phe1 phe CE2 phe1 phe CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_plane_atom.atom_id _item_description.description ; The id of an atom involved in the plane. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_plane_atom.atom_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_plane_atom.comp_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_comp_plane.id in the CHEM_COMP_PLANE category. ; _item.name '_chem_comp_plane_atom.plane_id' _item.mandatory_code yes save_ save__chem_comp_plane_atom.dist_esd _item_description.description ; This data item is the standard deviation of the out of plane distance for this atom. ; _item.name '_chem_comp_plane_atom.dist_esd' _item.mandatory_code no _item_type.code float _item_units.code 'angstroms' save_ #################### ## CHEM_COMP_TOR ## #################### save_CHEM_COMP_TOR _category.description ; Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. ; _category.id chem_comp_tor _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor.comp_id' '_chem_comp_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 phe phe_chi1 N CA CB CG phe phe_chi2 CA CB CG CD1 phe phe_ring1 CB CG CD1 CE1 phe phe_ring2 CB CG CD2 CE2 phe phe_ring3 CG CD1 CE1 CZ phe phe_ring4 CD1 CE1 CZ CE2 phe phe_ring5 CE1 CZ CE2 CD2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor.atom_id_1 _item_description.description ; The id of the first of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_2 _item_description.description ; The id of the second of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_3' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_3 _item_description.description ; The id of the third of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_4' save_ save__chem_comp_tor.atom_id_4 _item_description.description ; The id of the fourth of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_comp_tor.atom_id_1' '_chem_comp_tor.atom_id_2' '_chem_comp_tor.atom_id_3' save_ save__chem_comp_tor.id _item_description.description ; The value of _chem_comp_tor.id must uniquely identify a record in the CHEM_COMP_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp_tor.id' chem_comp_tor yes '_chem_comp_tor_value.tor_id' chem_comp_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_comp_tor_value.tor_id' '_chem_comp_tor.id' _item_type.code code save_ save__chem_comp_tor.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_chem_comp_tor.comp_id' _item.mandatory_code yes save_ ########################## ## CHEM_COMP_TOR_VALUE ## ########################## save_CHEM_COMP_TOR_VALUE _category.description ; Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_comp_tor_value _category.mandatory_code no loop_ _category_key.name '_chem_comp_tor_value.tor_id' '_chem_comp_tor_value.comp_id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _chem_comp_tor_value.tor_id _chem_comp_tor_value.comp_id _chem_comp_tor_value.angle _chem_comp_tor_value.dist phe_chi1 phe -60.0 2.88 phe_chi1 phe 180.0 3.72 phe_chi1 phe 60.0 2.88 phe_chi2 phe 90.0 3.34 phe_chi2 phe -90.0 3.34 phe_ring1 phe 180.0 3.75 phe_ring2 phe 180.0 3.75 phe_ring3 phe 0.0 2.80 phe_ring4 phe 0.0 2.80 phe_ring5 phe 0.0 2.80 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp_tor_value.comp_id _item_description.description ; This data item is a pointer to _chem_comp_atom.comp_id in the CHEM_COMP_ATOM category. ; _item.name '_chem_comp_tor_value.comp_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_comp_tor.id in the CHEM_COMP_TOR category. ; _item.name '_chem_comp_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_comp_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_comp_tor_value.angle' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_comp_tor_value.angle_esd _item_description.description ; The estimated standard deviation of _chem_comp_tor_value.angle. ; _item.name '_chem_comp_tor_value.angle_esd' _item.category_id chem_comp_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_comp_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_comp_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 will yield the same distance as a 60 degree angle). However the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_comp_tor_value.dist' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_comp_tor_value.dist_esd _item_description.description ; The estimated standard deviation of _chem_comp_tor_value.dist_esd. ; _item.name '_chem_comp_tor_value.dist_esd' _item.category_id chem_comp_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_comp_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############### ## CHEM_LINK ## ############### save_CHEM_LINK _category.description ; Data items in the CHEM_LINK category give details about the linkages between chemical groups. ; _category.id chem_link _category.mandatory_code no _category_key.name '_chem_link.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link.id _item_description.description ; The value of _chem_link.id must uniquely identify each item in the CHEM_LINK list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link.id' chem_link yes '_chem_link_angle.link_id' chem_link_angle yes '_chem_link_bond.link_id' chem_link_bond yes '_chem_link_chir.link_id' chem_link_chir yes '_chem_link_plane.link_id' chem_link_plane yes '_chem_link_tor.link_id' chem_link_tor yes '_chem_comp_link.link_id' chem_comp_link yes '_entity_link.link_id' entity_link yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_angle.link_id' '_chem_link.id' '_chem_link_bond.link_id' '_chem_link.id' '_chem_link_chir.link_id' '_chem_link.id' '_chem_link_plane.link_id' '_chem_link.id' '_chem_link_tor.link_id' '_chem_link.id' '_chem_comp_link.link_id' '_chem_link.id' '_entity_link.link_id' '_chem_link.id' _item_type.code code loop_ _item_examples.case 'peptide' 'oligosaccharide 1,4' 'DNA' save_ save__chem_link.details _item_description.description ; A description of special aspects of a linkage between chemical components in the structure. ; _item.name '_chem_link.details' _item.category_id chem_link _item.mandatory_code no _item_type.code text save_ ##################### ## CHEM_LINK_ANGLE ## ##################### save_CHEM_LINK_ANGLE _category.description ; Data items in the CHEM_LINK_ANGLE category record details about angles in a linkage between chemical groups. ; _category.id chem_link_angle _category.mandatory_code no loop_ _category_key.name '_chem_link_angle.link_id' '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh and Huber parameters as interpreted by J. P. Priestle ; ; loop_ _chem_link_angle.link_id _chem_link_angle.value_angle _chem_link_angle.value_angle_esd _chem_link_angle.atom_id_1 _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.atom_3_comp_id PEPTIDE 111.2 2.8 N 1 CA 1 C 1 PEPTIDE 120.8 1.7 CA 1 C 1 O 1 PEPTIDE 116.2 2.0 CA 1 C 1 N 2 PEPTIDE 123.0 1.6 O 1 C 1 N 2 PEPTIDE 121.7 1.8 C 1 N 2 CA 2 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_angle.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two component connected by the linkage. ; _item.name '_chem_link_angle.atom_1_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_2_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_angle.atom_2_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_angle.atom_3_comp_id' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_angle.atom_1_comp_id' '_chem_link_angle.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_angle.atom_id_1 _item_description.description ; The id of the first of the three atoms that define the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_angle.atom_id_1' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_2' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_2 _item_description.description ; The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_angle.atom_id_2' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_3' _item_type.code code save_ save__chem_link_angle.atom_id_3 _item_description.description ; The id of the third of the three atoms that define the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_angle.atom_id_3' _item.category_id chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_angle.atom_id_1' '_chem_link_angle.atom_id_2' _item_type.code code save_ save__chem_link_angle.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_angle.link_id' _item.mandatory_code yes save_ save__chem_link_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_angle.value_angle' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_angle.value_angle_esd _item_description.description ; The estimated standard deviation of _chem_link_angle.value_angle. ; _item.name '_chem_link_angle.value_angle_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_link_angle.value_dist' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_angle.value_dist_esd _item_description.description ; The estimated standard deviation of _chem_comp_angle.value_dist_esd. ; _item.name '_chem_link_angle.value_dist_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ #################### ## CHEM_LINK_BOND ## #################### save_CHEM_LINK_BOND _category.description ; Data items in the CHEM_LINK_BOND category record details about bonds in a linkage between components in the chemical structure. ; _category.id chem_link_bond _category.mandatory_code no loop_ _category_key.name '_chem_link_bond.link_id' '_chem_link_bond.atom_id_1' '_chem_link_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - Engh and Huber parameters as interpreted by J. P. Priestle ; ; loop_ _chem_link_bond.link_id _chem_link_bond.value_dist _chem_link_bond.value_dist_esd _chem_link_bond.atom_id_1 _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.atom_2_comp_id PEPTIDE 1.458 0.019 N 1 CA 1 PEPTIDE 1.525 0.021 CA 1 C 1 PEPTIDE 1.329 0.014 C 1 N 2 PEPTIDE 1.231 0.020 C 1 O 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_bond.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_bond.atom_1_comp_id' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_bond.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the linkage. ; _item.name '_chem_link_bond.atom_2_comp_id' _item.category_id chem_link_bond _item.mandatory_code no _item_dependent.dependent_name '_chem_link_bond.atom_1_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_bond.atom_id_1 _item_description.description ; The id of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_1' _item.category_id chem_link_bond _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_bond.atom_id_2' _item_type.code code save_ save__chem_link_bond.atom_id_2 _item_description.description ; The id of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_chem_link_bond.atom_id_2' _item.category_id chem_link_bond _item.mandatory_code yes _item_dependent.dependent_name '_chem_link_bond.atom_id_1' _item_type.code code save_ save__chem_link_bond.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_bond.link_id' _item.mandatory_code yes save_ save__chem_link_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_chem_link_bond.value_dist' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_bond.value_dist_esd _item_description.description ; The estimated standard deviation of _chem_link_bond.value_dist_esd. ; _item.name '_chem_link_bond.value_dist_esd' _item.category_id chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_bond.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__chem_link_bond.value_order _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. ; _item.name '_chem_link_bond.value_order' _item.category_id chem_link_bond _item.mandatory_code no _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalised double bond' pi 'pi bond' save_ #################### ## CHEM_LINK_CHIR ## #################### save_CHEM_LINK_CHIR _category.description ; Data items in the CHEM_LINK_CHIR category provide detail about the chiral centers in a linkage between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. ; _category.id chem_link_chir _category.mandatory_code no loop_ _category_key.name '_chem_link_chir.link_id' '_chem_link_chir.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_chir.atom_comp_id _item_description.description ; This data item indicates whether the chiral atom is found in the first or the second of the two component connected by the linkage. ; _item.name '_chem_link_chir.atom_comp_id' _item.category_id chem_link_chir _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir.atom_id _item_description.description ; The id of the atom that is a chiral center. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir.atom_config _item_description.description ; The chiral configuration of the atom that is a chiral center. ; _item.name '_chem_link_chir.atom_config' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail R 'absolute configuration R' S 'absolute configuration S' save_ save__chem_link_chir.id _item_description.description ; The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_chir.id' chem_link_chir yes '_chem_link_chir_atom.chir_id' chem_link_chir_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_chir_atom.chir_id' '_chem_link_chir.id' _item_type.code code save_ save__chem_link_chir.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_chir.link_id' _item.mandatory_code yes save_ save__chem_link_chir.number_atoms_all _item_description.description ; The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_all' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id. ; _item.name '_chem_link_chir.number_atoms_nh' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code int save_ save__chem_link_chir.volume_flag _item_description.description ; A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. ; _item.name '_chem_link_chir.volume_flag' _item.category_id chem_link_chir _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sign 'match magnitude and sign' nosign 'match magnitude only' save_ save__chem_link_chir.volume_three _item_description.description ; The chiral volume V(c), for chiral centers that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product ; _item.name '_chem_link_chir.volume_three' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms_cubed save_ save__chem_link_chir.volume_three_esd _item_description.description ; The estimated standard deviation of _chem_link_chir.volume_three. ; _item.name '_chem_link_chir.volume_three_esd' _item.category_id chem_link_chir _item.mandatory_code no _item_related.related_name '_chem_link_chir.volume_three' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms_cubed save_ ######################### ## CHEM_LINK_CHIR_ATOM ## ######################### save_CHEM_LINK_CHIR_ATOM _category.description ; Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a linkage between two chemical components. ; _category.id chem_link_chir_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_chir_atom.chir_id' '_chem_link_chir_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_chir_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_chir_atom.atom_comp_id' _item.category_id chem_link_chir_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_chir_atom.atom_id _item_description.description ; The id of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_chir_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_chir_atom.chir_id _item_description.description ; This data item is a pointer to _chem_link_chir.id in the CHEM_LINK_CHIR category. ; _item.name '_chem_link_chir_atom.chir_id' _item.mandatory_code yes save_ save__chem_link_chir_atom.dev _item_description.description ; The estimated standard deviation of the position of this atom from the plane defined by all of the atoms in the plane. ; _item.name '_chem_link_chir_atom.dev' _item.category_id chem_link_chir_atom _item.mandatory_code no _item_type.code float _item_units.code angstroms save_ ###################### ## CHEM_LINK_PLANE ## ###################### save_CHEM_LINK_PLANE _category.description ; Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a linkage between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. ; _category.id chem_link_plane _category.mandatory_code no loop_ _category_key.name '_chem_link_plane.link_id' '_chem_link_plane.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_plane.id _item_description.description ; The value of _chem_link_plane.id must uniquely identify a record in the CHEM_LINK_PLANE list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_plane.id' chem_link_plane yes '_chem_link_plane_atom.plane_id' chem_link_plane_atom yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_plane_atom.plane_id' '_chem_link_plane.id' _item_type.code code save_ save__chem_link_plane.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_plane.link_id' _item.mandatory_code yes save_ save__chem_link_plane.number_atoms_all _item_description.description ; The total number of atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_all' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ save__chem_link_plane.number_atoms_nh _item_description.description ; The number of non-hydrogen atoms in the plane. ; _item.name '_chem_link_plane.number_atoms_nh' _item.category_id chem_link_plane _item.mandatory_code no _item_type.code int save_ ########################### ## CHEM_LINK_PLANE_ATOM ## ########################### save_CHEM_LINK_PLANE_ATOM _category.description ; Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a linkage between two chemical components. ; _category.id chem_link_plane_atom _category.mandatory_code no loop_ _category_key.name '_chem_link_plane_atom.plane_id' '_chem_link_plane_atom.atom_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_plane_atom.atom_comp_id _item_description.description ; This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_plane_atom.atom_comp_id' _item.category_id chem_link_plane_atom _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_plane_atom.atom_id _item_description.description ; The id of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_plane_atom.atom_id' _item.mandatory_code yes _item_type.code code save_ save__chem_link_plane_atom.plane_id _item_description.description ; This data item is a pointer to _chem_link_plane.id in the CHEM_LINK_PLANE category. ; _item.name '_chem_link_plane_atom.plane_id' _item.mandatory_code yes save_ #################### ## CHEM_LINK_TOR ## #################### save_CHEM_LINK_TOR _category.description ; Data items in the CHEM_LINK_TOR category record details about the torsion angles in a linkage between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. ; _category.id chem_link_tor _category.mandatory_code no loop_ _category_key.name '_chem_link_tor.link_id' '_chem_link_tor.id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_tor.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_tor.atom_1_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_tor.atom_2_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_3_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_tor.atom_3_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_4_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_4_comp_id _item_description.description ; This data item indicates whether atom 4 is found in the first or the second of the two components connected by the linkage. ; _item.name '_chem_link_tor.atom_4_comp_id' _item.category_id chem_link_tor _item.mandatory_code no loop_ _item_dependent.dependent_name '_chem_link_tor.atom_1_comp_id' '_chem_link_tor.atom_2_comp_id' '_chem_link_tor.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__chem_link_tor.atom_id_1 _item_description.description ; The id of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_2 _item_description.description ; The id of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_3' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_3 _item_description.description ; The id of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_4' _item_type.code code save_ save__chem_link_tor.atom_id_4 _item_description.description ; The id of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_chem_link_tor.atom_id_4' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_chem_link_tor.atom_id_1' '_chem_link_tor.atom_id_2' '_chem_link_tor.atom_id_3' _item_type.code code save_ save__chem_link_tor.id _item_description.description ; The value of _chem_link_tor.id must uniquely identify a record in the CHEM_LINK_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_link_tor.id' chem_link_tor yes '_chem_link_tor_value.tor_id' chem_link_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_chem_link_tor_value.tor_id' '_chem_link_tor.id' _item_type.code code save_ save__chem_link_tor.link_id _item_description.description ; This data item is a pointer to _chem_link.id in the CHEM_LINK category. ; _item.name '_chem_link_tor.link_id' _item.mandatory_code yes save_ ########################## ## CHEM_LINK_TOR_VALUE ## ########################## save_CHEM_LINK_TOR_VALUE _category.description ; Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. ; _category.id chem_link_tor_value _category.mandatory_code no _category_key.name '_chem_link_tor_value.tor_id' loop_ _category_group.id 'inclusive_group' 'chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_link_tor_value.tor_id _item_description.description ; This data item is a pointer to _chem_link_tor.id in the CHEM_LINK_TOR category. ; _item.name '_chem_link_tor_value.tor_id' _item.mandatory_code yes save_ save__chem_link_tor_value.angle _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. ; _item.name '_chem_link_tor_value.angle' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_tor_value.angle_esd _item_description.description ; The estimated standard deviation of _chem_link_tor_value.angle. ; _item.name '_chem_link_tor_value.angle_esd' _item.category_id chem_link_tor_value _item.mandatory_code yes loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 -180.0 -180.0 -180.0 _item_related.related_name '_chem_link_tor_value.angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_tor_value.dist _item_description.description ; A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 will yield the same distance as a 60 degree angle). However the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. ; _item.name '_chem_link_tor_value.dist' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_tor_value.dist_esd _item_description.description ; The estimated standard deviation of _chem_link_tor_value.dist_esd. ; _item.name '_chem_link_tor_value.dist_esd' _item.category_id chem_link_tor_value _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_tor_value.dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ############## ## CHEMICAL ## ############## save_CHEMICAL _category.description ; Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. ; _category.id chemical _category.mandatory_code no _category_key.name '_chemical.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical.entry_id' _item.mandatory_code yes save_ save__chemical.compound_source _item_description.description ; Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. ; _item.name '_chemical.compound_source' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_compound_source' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'From Norilsk (USSR)' 'Extracted from the bark of Cinchona Naturalis' save_ save__chemical.melting_point _item_description.description ; The temperature in kelvins at which a crystalline solid changes to a liquid. ; _item.name '_chemical.melting_point' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_melting_point' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code kelvin save_ save__chemical.name_common _item_description.description ; Trivial name by which the compound is commonly known. ; _item.name '_chemical.name_common' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_common' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case '1-bromoestradiol' save_ save__chemical.name_mineral _item_description.description ; Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical.compound_source. ; _item.name '_chemical.name_mineral' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_mineral' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'chalcopyrite' save_ save__chemical.name_structure_type _item_description.description ; Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. ; _item.name '_chemical.name_structure_type' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_structure_type' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'perovskite' 'sphalerite' 'A15' save_ save__chemical.name_systematic _item_description.description ; IUPAC or Chemical Abstracts full name of compound. ; _item.name '_chemical.name_systematic' _item.category_id chemical _item.mandatory_code no _item_aliases.alias_name '_chemical_name_systematic' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol' save_ ######################## ## CHEMICAL_CONN_ATOM ## ######################## save_CHEMICAL_CONN_ATOM _category.description ; Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. ; _category.id chemical_conn_atom _category.mandatory_code no _category_key.name '_chemical_conn_atom.number' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_atom.charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_chemical_conn_atom.charge' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_charge' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 6 6 6 -6 -6 -6 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__chemical_conn_atom.display_x _item_description.description ; The 2D Cartesian x coordinate of the position of this atom in a recognisable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journal or database staff. ; _item.name '_chemical_conn_atom.display_x' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_x' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_dependent.dependent_name '_chemical_conn_atom.display_y' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.display_y _item_description.description ; The 2D Cartesian y coordinate of the position of this atom in a recognisable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. If absent, values will be assigned by the journal or database staff. ; _item.name '_chemical_conn_atom.display_y' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_display_y' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_dependent.dependent_name '_chemical_conn_atom.display_x' loop_ _item_range.maximum _item_range.minimum 1.0 1.0 1.0 0.0 0.0 0.0 _item_type.code float save_ save__chemical_conn_atom.NCA _item_description.description ; The number of connected atoms excluding terminal hydrogen atoms. ; _item.name '_chemical_conn_atom.NCA' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NCA' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.NH _item_description.description ; The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the ATOM_SITE list. ; _item.name '_chemical_conn_atom.NH' _item.category_id chemical_conn_atom _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_atom_NH' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0 0 0 _item_type.code int save_ save__chemical_conn_atom.number _item_description.description ; The chemical sequence number to be associated with this atom. Within an ATOM_SITE list this number must match with one of the _atom_site.chemical_conn_number values. ; loop_ _item.name _item.category_id _item.mandatory_code '_chemical_conn_atom.number' chemical_conn_atom yes '_atom_site.chemical_conn_number' atom_site no '_chemical_conn_bond.atom_1' chemical_conn_bond yes '_chemical_conn_bond.atom_2' chemical_conn_bond yes _item_aliases.alias_name '_chemical_conn_atom_number' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.chemical_conn_number' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_1' '_chemical_conn_atom.number' '_chemical_conn_bond.atom_2' '_chemical_conn_atom.number' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ save__chemical_conn_atom.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_chemical_conn_atom.type_symbol' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_atom_type_symbol' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ ######################## ## CHEMICAL_CONN_BOND ## ######################## save_CHEMICAL_CONN_BOND _category.description ; Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the 2D chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the _chemical_conn_atom. list and the nature of the chemical bond between these atoms. ; _category.id chemical_conn_bond _category.mandatory_code no loop_ _category_key.name '_chemical_conn_bond.atom_1' '_chemical_conn_bond.atom_2' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_conn_bond.atom_1 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_1' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_1' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_dependent.dependent_name '_chemical_conn_bond.atom_2' save_ save__chemical_conn_bond.atom_2 _item_description.description ; This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category. ; _item.name '_chemical_conn_bond.atom_2' _item.mandatory_code yes _item_aliases.alias_name '_chemical_conn_bond_atom_2' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_dependent.dependent_name '_chemical_conn_bond.atom_1' save_ save__chemical_conn_bond.type _item_description.description ; The chemical bond type associated with the connection between the two sites _chemical_conn_bond.atom_1 and _chemical_conn_bond.atom_2. ; _item.name '_chemical_conn_bond.type' _item.category_id chemical_conn_bond _item.mandatory_code no _item_aliases.alias_name '_chemical_conn_bond_type' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_default.value sing _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail sing 'single bond' doub 'double bond' trip 'triple bond' quad 'quadruple bond' arom 'aromatic bond' poly 'polymeric bond' delo 'delocalised double bond' pi 'pi bond' save_ ###################### ## CHEMICAL_FORMULA ## ###################### save_CHEMICAL_FORMULA _category.description ; Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count. 4. Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers. [An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units]. 5. Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, H followed by the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. ; _category.id chemical_formula _category.mandatory_code no _category_key.name '_chemical_formula.entry_id' loop_ _category_group.id 'inclusive_group' 'chemical_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _chemical_formula.entry_id 'TOZ' _chemical_formula.moiety 'C18 H25 N O3' _chemical_formula.sum 'C18 H25 N O3' _chemical_formula.weight 303.40 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chemical_formula.analytical _item_description.description ; Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (e.s.d.'s). ; _item.name '_chemical_formula.analytical' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_analytical' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'Fe2.45(2) Ni1.60(3) S4' save_ save__chemical_formula.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_chemical_formula.entry_id' _item.mandatory_code yes save_ save__chemical_formula.iupac _item_description.description ; Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other _chemical_formula_ entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other _chemical_formula_ data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. ; _item.name '_chemical_formula.iupac' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_iupac' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' save_ save__chemical_formula.moiety _item_description.description ; Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORUMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: 1. Moieties are separated by commas ','. 2. The order of elements within a moiety follows general rule 5 in the CHEMICAL_FORMULA category description. 3. Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. 4. Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. ; _item.name '_chemical_formula.moiety' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_moiety' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'C7 H4 Cl Hg N O3 S' 'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-' 'C12 H16 N2 O6, 5(H2 O1)' "(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)" save_ save__chemical_formula.structural _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom type and atom site data should not be included in this formula (see also _chemical_formula.analytical). ; _item.name '_chemical_formula.structural' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_structural' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'Ca ((Cl O3)2 O)2 (H2 O)6' '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' save_ save__chemical_formula.sum _item_description.description ; See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule 5 in the CHEMICAL_FORMULA category description. Parentheses are not normally used. ; _item.name '_chemical_formula.sum' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_sum' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chemical_formula.weight _item_description.description ; Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula.structural, chemical_formula.moiety or chemical_forumula.sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal.density_diffrn. ; _item.name '_chemical_formula.weight' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chemical_formula.weight_meas _item_description.description ; Formula mass in daltons measured by a non-diffraction experiment. ; _item.name '_chemical_formula.weight_meas' _item.category_id chemical_formula _item.mandatory_code no _item_aliases.alias_name '_chemical_formula_weight_meas' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ############## ## CITATION ## ############## save_CITATION _category.description ; Data items in the CITATION category record details about the literature cited relevant to the contents of the data block. ; _category.id citation _category.mandatory_code no _category_key.name '_citation.id' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _citation.id _citation.coordinate_linkage _citation.title _citation.country _citation.journal_abbrev _citation.journal_volume _citation.journal_issue _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_title _citation.book_publisher _citation.book_coden_ISBN _citation.details primary yes ; Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution. ; US 'J. Biol. Chem.' 265 . 14209 14219 1990 HBCHA3 0021-9258 071 . . . ; The publication that directly relates to this coordinate set. ; 2 no ; Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1. ; UK 'Nature' 337 . 615 619 1989 NATUAS 0028-0836 006 . . . ; Determination of the structure of the unliganded enzyme. ; 3 no ; Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1. ; US 'J. Biol. Chem.' 264 . 1919 1921 1989 HBCHA3 0021-9258 071 . . . ; Crystallization of the unliganded enzyme. ; 4 no ; Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease. ; US 'J. Biol. Chem.' 264 . 2307 2312 1989 HBCHA3 0021-9258 071 . . . ; Expression and purification of the enzyme. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation.abstract _item_description.description ; Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. ; _item.name '_citation.abstract' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__citation.abstract_id_CAS _item_description.description ; The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. ; _item.name '_citation.abstract_id_CAS' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_abstract_id_CAS' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__citation.book_id_ISBN _item_description.description ; The International Standard Book Number (ISBN) code assigned to the book cited; relevant for book chapters. ; _item.name '_citation.book_id_ISBN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_id_ISBN' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.book_publisher _item_description.description ; The name of the publisher of the citation; relevant for book chapters. ; _item.name '_citation.book_publisher' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'John Wiley and Sons' save_ save__citation.book_publisher_city _item_description.description ; The location of the publisher of the citation; relevant for book chapters. ; _item.name '_citation.book_publisher_city' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher_city' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'London' save_ save__citation.book_title _item_description.description ; The title of the book in which the citation appeared; relevant for book chapters. ; _item.name '_citation.book_title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_title' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__citation.coordinate_linkage _item_description.description ; _citation.coordinate_linkage states whether or not this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to creation of the data block, the value of this data item would be 'no'. ; _item.name '_citation.coordinate_linkage' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_coordinate_linkage' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'citation not directly linked to coordinates' n 'abbreviation for "no"' yes 'citation directly linked to coordinates' y 'abbreviation for "yes"' save_ save__citation.country _item_description.description ; The country of publication; relevant for both journal articles and book chapters. ; _item.name '_citation.country' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_country' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.database_id_Medline _item_description.description ; Ascession number used by Medline to categorize a specific bibliographic entry. ; _item.name '_citation.database_id_Medline' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_database_id_Medline' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int _item_examples.case 89064067 save_ save__citation.details _item_description.description ; A description of special aspects that describe the relationship of the contents of the data block to the literature item cited. ; _item.name '_citation.details' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_special_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case ; citation relates to this precise coordinate set ; ; citation relates to earlier low-resolution structure ; ; citation relates to further refinement of structure reported in citation 2 ; save_ save__citation.id _item_description.description ; The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_citation.id' citation yes '_citation_author.citation_id' citation_author yes '_citation_editor.citation_id' citation_editor yes '_software.citation_id' software yes _item_aliases.alias_name '_citation_id' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_linked.child_name _item_linked.parent_name '_citation_author.citation_id' '_citation.id' '_citation_editor.citation_id' '_citation.id' '_software.citation_id' '_citation.id' _item_type.code code loop_ _item_examples.case 'primary' '1' '2' save_ save__citation.journal_abbrev _item_description.description ; Abbreviated name of the journal cited as given in the Chemical Abstracts Service Source Index. ; _item.name '_citation.journal_abbrev' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_abbrev' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case 'J. Mol. Biol.' save_ save__citation.journal_id_ASTM _item_description.description ; The American Society for the Testing of Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. ; _item.name '_citation.journal_id_ASTM' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ASTM' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.journal_id_CSD _item_description.description ; The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Brookhaven Protein Data Bank (PDB). ; _item.name '_citation.journal_id_CSD' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_CSD' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case '070' save_ save__citation.journal_id_ISSN _item_description.description ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_id_ISSN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ISSN' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.journal_full _item_description.description ; Full name of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_full' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'Journal of Molecular Biology' save_ save__citation.journal_issue _item_description.description ; Issue number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_issue' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_issue' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case '2' save_ save__citation.journal_volume _item_description.description ; Volume number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_volume' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_volume' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case '174' save_ save__citation.language _item_description.description ; Language in which the citation appears. ; _item.name '_citation.language' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_language' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line _item_examples.case 'german' save_ save__citation.page_first _item_description.description ; The first page of the citation; relevant for journal articles and book chapters. ; _item.name '_citation.page_first' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_first' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.page_last _item_description.description ; The last page of the citation; relevant for journal articles and book chapters. ; _item.name '_citation.page_last' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_last' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__citation.title _item_description.description ; The title of the citation; relevant for both journal articles and book chapters. ; _item.name '_citation.title' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_title' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; Structure of Blah-Blah at 2.1 \%Angstr\"om Resolution. ; save_ save__citation.year _item_description.description ; The year of the citation; relevant for both journal articles and book chapters. ; _item.name '_citation.year' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_year' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code int _item_examples.case 1984 save_ ##################### ## CITATION_AUTHOR ## ##################### save_CITATION_AUTHOR _category.description ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. ; _category.id citation_author _category.mandatory_code no loop_ _category_key.name '_citation_author.citation_id' '_citation_author.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and/or laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _citation_author.citation_id _citation_author.ordinal _citation_author.name primary 1 'Fitzgerald, P.M.D.' primary 2 'McKeever, B.M.' primary 3 'Van Middlesworth, J.F.' primary 4 'Springer, J.P.' primary 5 'Heimbach, J.C.' primary 6 'Leu, C.-T.' primary 7 'Herber, W.K.' primary 8 'Dixon, R.A.F.' primary 9 'Darke, P.L.' 2 1 'Navia, M.A.' 2 2 'Fitzgerald, P.M.D.' 2 3 'McKeever, B.M.' 2 4 'Leu, C.-T.' 2 5 'Heimbach, J.C.' 2 6 'Herber, W.K.' 2 7 'Sigal, I.S.' 2 8 'Darke, P.L.' 2 9 'Springer, J.P.' 3 1 'McKeever, B.M.' 3 2 'Navia, M.A.' 3 3 'Fitzgerald, P.M.D.' 3 4 'Springer, J.P.' 3 5 'Leu, C.-T.' 3 6 'Heimbach, J.C.' 3 7 'Herber, W.K.' 3 8 'Sigal, I.S.' 3 9 'Darke, P.L.' 4 1 'Darke, P.L.' 4 2 'Leu, C.-T.' 4 3 'Davis, L.J.' 4 4 'Heimbach, J.C.' 4 5 'Diehl, R.E.' 4 6 'Hill, W.S.' 4 7 'Dixon, R.A.F.' 4 8 'Sigal, I.S.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_author.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_author.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_author_citation_id' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__citation_author.name _item_description.description ; Name of an author of the citation; relevant for both journal articles and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_author.name' _item.category_id citation_author _item.mandatory_code yes _item_aliases.alias_name '_citation_author_name' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__citation_author.ordinal _item_description.description ; This data item defines the order of the author's name in the list of authors of a citation. ; _item.name '_citation_author.ordinal' _item.category_id citation_author _item.mandatory_code no _item_aliases.alias_name '_citation_author_ordinal' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code int save_ ##################### ## CITATION_EDITOR ## ##################### save_CITATION_EDITOR _category.description ; Data items in the CITATION_EDITOR category record details about the editor associated with book chapter citations in the CITATION list. ; _category.id citation_editor _category.mandatory_code no loop_ _category_key.name '_citation_editor.citation_id' '_citation_editor.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - example is completely hypothetical ; ; loop_ _citation_editor.citation_id _citation_editor.name 5 'McKeever, B.M.' 5 'Navia, M.A.' 5 'Fitzgerald, P.M.D.' 5 'Springer, J.P.' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_editor.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_editor.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_editor_citation_id' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 save_ save__citation_editor.name _item_description.description ; Names of an editor of the citation; relevant for book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_editor.name' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_name' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__citation_editor.ordinal _item_description.description ; This data item defines the order of the editor's name in the list of editors of a citation. ; _item.name '_citation_editor.ordinal' _item.category_id citation_editor _item.mandatory_code no _item_aliases.alias_name '_citation_editor_ordinal' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code int save_ ############### ## COMPUTING ## ############### save_COMPUTING _category.description ; Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. ; _category.id computing _category.mandatory_code no _category_key.name '_computing.entry_id' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _computing.entry_id '5HVP' _computing.data_collection 'Collect (Siemens)' _computing.data_reduction 'Xengen (Howard)' _computing.molecular_graphics 'Protein (Steigemann), Frodo (Jones)' _computing.structure_refinement ; Protin/Prolsq (Konnert, Hendrickson) ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _computing.data_collection 'Philips PW1100/20 software 1976' _computing.cell_refinement 'LATCON (Xtal: Schwarzenbach & King)' _computing.data_reduction 'pwredu (McLaughlin) ADDREF SORTRF (Xtal)' _computing.structure_solution 'SHELXS86 (Sheldrick)' _computing.structure_refinement 'SHELX76 (Sheldrick) CRYLSQ (Xtal: Olthof)' _computing.publication_material 'BONDLA CIFIO (Xtal: Hall)' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__computing.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_computing.entry_id' _item.mandatory_code yes save_ save__computing.cell_refinement _item_description.description ; Software used in refining the cell. Give the program or package name and a brief reference. ; _item.name '_computing.cell_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_cell_refinement' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'CAD4 (Enraf Nonius)' save_ save__computing.data_collection _item_description.description ; Software used for data collection. Give the program or package name and a brief reference. ; _item.name '_computing.data_collection' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_collection' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'CAD4 (Enraf Nonius)' save_ save__computing.data_reduction _item_description.description ; Software used for data reduction. Give the program or package name and a brief reference. ; _item.name '_computing.data_reduction' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_data_reduction' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'DIFDAT, SORTRF, ADDREF (XTAL3.0, 1990)' save_ save__computing.molecular_graphics _item_description.description ; Software used for molecular graphics. Give the program or package name and a brief reference. ; _item.name '_computing.molecular_graphics' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_molecular_graphics' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'FRODO (Jones, 1986) & ORTEP (Johnson, 1965)' save_ save__computing.publication_material _item_description.description ; Software used for generating material for publication. Give the program or package name and a brief reference. ; _item.name '_computing.publication_material' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_publication_material' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__computing.structure_refinement _item_description.description ; Software used for refinement of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_refinement' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_refinement' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'SHELX85 (Sheldrick, 1985)' 'X-PLOR (Brunger, 198?)' save_ save__computing.structure_solution _item_description.description ; Software used for solution of the structure. Give the program or package name and a brief reference. ; _item.name '_computing.structure_solution' _item.category_id computing _item.mandatory_code no _item_aliases.alias_name '_computing_structure_solution' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case 'SHELX85 (Sheldrick, 1985)' save_ ############## ## DATABASE ## ############## save_DATABASE _category.description ; Data items in the DATABASE category have been superseded by data items in the DATEBASE_NEW category. They are included here only for compliance with older files. ; _category.id database _category.mandatory_code no _category_key.name '_database.entry_id' loop_ _category_group.id 'inclusive_group' 'compliance_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on ; ; Need example 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database.entry_id' _item.mandatory_code yes save_ save__database.code_CAS _item_description.description ; The code assigned by Chemical Abstracts. ; _item.name '_database.code_CAS' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_CAS' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.code_CSD _item_description.description ; The code assigned by Cambridge Structural Database (organic and metal-organic compounds). ; _item.name '_database.code_CSD' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_CSD' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.code_ICSD _item_description.description ; The code assigned by the Inorganic Crystal Structure Data Base. ; _item.name '_database.code_ICSD' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_ICSD' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.code_MDF _item_description.description ; The code assigned by the Metals Data File (metal structures). ; _item.name '_database.code_MDF' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_MDF' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.code_NBS _item_description.description ; The code assigned by the NBS (NIST) Crystal Data Database (lattice parameters). ; _item.name '_database.code_NBS' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_NBS' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.code_PDF _item_description.description ; The code assigned by the Powder Diffraction File (JCPDS/ICDD). ; _item.name '_database.code_PDF' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_code_PDF' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_related.related_name _item_related.function_code '_database_2.database_id' 'replacedby' '_database_2.database_code' 'replacedby' _item_type.code line save_ save__database.journal_ASTM _item_description.description ; The ASTM CODEN designatorfor a journal as given in the Chemical Source List maintained by the Chemical Astracts Service. ; _item.name '_database.journal_ASTM' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_ASTM' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__database.journal_CSD _item_description.description ; The journal code used in the Cambridge Structural Database. ; _item.name '_database.journal_CSD' _item.category_id database _item.mandatory_code no _item_aliases.alias_name '_database_journal_CSD' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ ################ ## DATABASE_2 ## ################ save_DATABASE_2 _category.description ; Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The somewhat clunky name of this category (DATABASE_2) is a consequence of the name DATABASE having been already used in the CIF core, but used in a manner different than the usage in mmCIF. Since CIF data names, once adopted, cannot be changed, a new category was created. ; _category.id database_2 _category.mandatory_code no loop_ _category_key.name '_database_2.database_id' '_database_2.database_code' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _database_2.database_id 'PDB' _database_2.database_code '5HVP' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_2.database_id _item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_2.database_id' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' 'replaces' '_database.code_CSD' 'replaces' '_database.code_ICSD' 'replaces' '_database.code_MDF' 'replaces' '_database.code_NBS' 'replaces' '_database.code_PDF' 'replaces' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail CAS ; Chemical Abstracts ; CSD ; Cambridge Structural Database (organic and metal-organic compounds) ; ICSD ; Inorganic Crystal Structure Data Base ; MDF ; Metals Data File (metal structures) ; NDB ; Nucleic Acid Database ; NBS ; NBS (NIST) Crystal Data Database (lattice parameters) ; PDB ; Protein Data Bank ; PDF ; Powder Diffraction File (JCPDS/ICDD) ; save_ save__database_2.database_code _item_description.description ; The code assigned by the database identified in _database_2.database_id. ; _item.name '_database_2.database_code' _item.category_id database_2 _item.mandatory_code yes loop_ _item_related.related_name _item_related.function_code '_database.code_CAS' 'replaces' '_database.code_CSD' 'replaces' '_database.code_ICSD' 'replaces' '_database.code_MDF' 'replaces' '_database.code_NBS' 'replaces' '_database.code_PDF' 'replaces' _item_type.code line loop_ _item_examples.case 1ABC ABCDEF save_ ######################### ## DATABASE_PDB_CAVEAT ## ######################### save_DATABASE_PDB_CAVEAT _category.description ; Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_caveat _category.mandatory_code no _category_key.name '_database_PDB_caveat.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - completely hypothetical ; ; loop_ _database_PDB_caveat.id _database_PDB_caveat.text 1 ; CAVEAT 1ABC THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS ; 2 ; CAVEAT 2 1ABC UNCORRECTABLE AT THIS TIME ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_caveat.id _item_description.description ; A unique identifier for the PDB caveat record. ; _item.name '_database_PDB_caveat.id' _item.category_id database_PDB_caveat _item.mandatory_code yes _item_type.code int save_ save__database_PDB_caveat.text _item_description.description ; The full text of the PDB caveat record. ; _item.name '_database_PDB_caveat.text' _item.category_id database_PDB_caveat _item.mandatory_code no _item_type.code text save_ ######################### ## DATABASE_PDB_MATRIX ## ######################### save_DATABASE_PDB_MATRIX _category.description ; The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_pdb_matrix _category.mandatory_code no _category_key.name '_database_pdb_matrix.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_pdb_matrix.entry_id _item_description.description ; This data item is a pointer to _entry.id in the ENTRY category. ; _item.name '_database_pdb_matrix.entry_id' _item.mandatory_code yes save_ save__database_pdb_matrix.origx[1][1] _item_description.description ; The [1][1] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[1][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[1][2] _item_description.description ; The [1][2] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[1][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[1][3] _item_description.description ; The [1][3] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[1][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[2][1] _item_description.description ; The [2][1] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[2][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[2][2] _item_description.description ; The [2][2] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[2][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[2][3] _item_description.description ; The [2][3] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[2][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[3][1] _item_description.description ; The [3][1] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[3][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[3][2] _item_description.description ; The [3][2] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[3][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx[3][3] _item_description.description ; The [1][1] element of the PDB ORIGX matrix. ; _item.name '_database_pdb_matrix.origx[3][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.origx_vector[1] _item_description.description ; The [1] element of the PDB ORIGX vector. ; _item.name '_database_pdb_matrix.origx_vector[1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_matrix.origx_vector[2] _item_description.description ; The [2] element of the PDB ORIGX vector. ; _item.name '_database_pdb_matrix.origx_vector[2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_matrix.origx_vector[3] _item_description.description ; The [3] element of the PDB ORIGX vector. ; _item.name '_database_pdb_matrix.origx_vector[3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_matrix.scale[1][1] _item_description.description ; The [1][1] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[1][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[1][2] _item_description.description ; The [1][2] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[1][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[1][3] _item_description.description ; The [1][3] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[1][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[2][1] _item_description.description ; The [2][1] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[2][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[2][2] _item_description.description ; The [2][2] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[2][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[2][3] _item_description.description ; The [2][3] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[2][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[3][1] _item_description.description ; The [3][1] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[3][1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[3][2] _item_description.description ; The [3][2] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[3][2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale[3][3] _item_description.description ; The [1][1] element of the PDB SCALE matrix. ; _item.name '_database_pdb_matrix.scale[3][3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 1.0 _item_sub_category.id matrix _item_type.code float save_ save__database_pdb_matrix.scale_vector[1] _item_description.description ; The [1] element of the PDB SCALE vector. ; _item.name '_database_pdb_matrix.scale_vector[1]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_matrix.scale_vector[2] _item_description.description ; The [2] element of the PDB SCALE vector. ; _item.name '_database_pdb_matrix.scale_vector[2]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_matrix.scale_vector[3] _item_description.description ; The [3] element of the PDB SCALE vector. ; _item.name '_database_pdb_matrix.scale_vector[3]' _item.category_id database_pdb_matrix _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ######################### ## DATABASE_PDB_REMARK ## ######################### save_DATABASE_PDB_REMARK _category.description ; Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_PDB_remark _category.mandatory_code no _category_key.name '_database_PDB_remark.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _database_PDB_remark.id _database_PDB_remark.text 3 ; REMARK 3 5HVP REMARK 3 REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. 5HVP REMARK 3 KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R 5HVP REMARK 3 VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION 5HVP REMARK 3 RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). 5HVP REMARK 3 5HVP REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 5HVP REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 5HVP REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 5HVP REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS) 5HVP REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS) 5HVP REMARK 3 BOND DISTANCE 0.018(0.020) 5HVP REMARK 3 ANGLE DISTANCE 0.038(0.030) 5HVP REMARK 3 PLANAR 1-4 DISTANCE 0.043(0.040) 5HVP REMARK 3 PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) 5HVP REMARK 3 CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) 5HVP REMARK 3 NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) 5HVP REMARK 3 SINGLE TORSION CONTACT 0.216(0.500) 5HVP REMARK 3 MULTIPLE TORSION CONTACT 0.207(0.500) 5HVP REMARK 3 POSSIBLE HYDROGEN BOND 0.245(0.500) 5HVP REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) 5HVP REMARK 3 PLANAR (OMEGA) 2.6(3.0) 5HVP REMARK 3 STAGGERED 17.4(15.0) 5HVP REMARK 3 ORTHONORMAL 18.1(20.0) 5HVP ; 4 ; REMARK 4 5HVP REMARK 4 THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE 5HVP REMARK 4 THE CHAIN INDICATORS *A* AND *B*. 5HVP ; # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_remark.id _item_description.description ; A unique identifier for the PDB remark record. ; _item.name '_database_PDB_remark.id' _item.category_id database_PDB_remark _item.mandatory_code yes _item_type.code int save_ save__database_PDB_remark.text _item_description.description ; The full text of the PDB remark record. ; _item.name '_database_PDB_remark.text' _item.category_id database_PDB_remark _item.mandatory_code no _item_type.code text save_ ###################### ## DATABASE_PDB_REV ## ###################### save_DATABASE_PDB_REV _category.description ; Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev _category.mandatory_code no _category_key.name '_database_PDB_rev.num' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; loop_ _database_PDB_rev.num _database_PDB_rev.author_name _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.mod_type 1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30 'full release' 0 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev.author_name _item_description.description ; The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma, precedes the first name(s) or initial(s). ; _item.name '_database_PDB_rev.author_name' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' save_ save__database_PDB_rev.date _item_description.description ; Date the PDB revision took place. Taken from the REVDAT record. ; _item.name '_database_PDB_rev.date' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd save_ save__database_PDB_rev.date_original _item_description.description ; Date the entry first entered the PDB database in the form: yyyy-mm-dd. Taken from the PDB HEADER record. ; _item.name '_database_PDB_rev.date_original' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case '1980-08-21' save_ save__database_PDB_rev.mod_type _item_description.description ; Taken from the REVDAT record. Refer to the Protein Data Bank format description for details. ; _item.name '_database_PDB_rev.mod_type' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code int loop_ _item_enumeration.value _item_enumeration.detail 0 'initial entry' 1 'all other types of modification' 2 'modifications to CONECT records' 3 ; modifications affecting the coordinates or their transforms (CRYST1, ORIGX, SCALE, MTRIX, TVECT, ATOM, HETATM, SIGATM records) ; save_ save__database_PDB_rev.num _item_description.description ; The value of _database_PDB_rev.num must uniquely and sequentially identify a record in the _database_PDB_rev. list. Note that this item must be a number, and that modification numbers are assigned in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_database_PDB_rev.num' database_PDB_rev yes '_database_PDB_rev_record.rev_num' database_PDB_rev_record yes loop_ _item_linked.child_name _item_linked.parent_name '_database_PDB_rev_record.rev_num' '_database_PDB_rev.num' _item_type.code int save_ save__database_PDB_rev.replaced_by _item_description.description ; The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaced_by' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.replaces _item_description.description ; The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. ; _item.name '_database_PDB_rev.replaces' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code line save_ save__database_PDB_rev.status _item_description.description ; This definition is preliminary - need to consult with PDB about what they need here. ; _item.name '_database_PDB_rev.status' _item.category_id database_PDB_rev _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value 'in preparation' 'prerelease' 'full release' 'obsolete' save_ ############################# ## DATABASE_PDB_REV_RECORD ## ############################# save_DATABASE_PDB_REV_RECORD _category.description ; Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. ; _category.id database_PDB_rev_record _category.mandatory_code no _category_key.name '_database_PDB_rev_record.rev_num' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - example is completely hypothetical ; ; loop_ _database_PDB_rev_record.rev_num _database_PDB_rev_record.type _database_PDB_rev_record.details 1 CONECT 'Error fix - incorrect connection between atoms 2312 and 2317' 2 MATRIX 'For consistency with 1995-08-04 style-guide' 3 ORIGX 'Based on new data from author' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_PDB_rev_record.details _item_description.description ; A description of special aspects of the revision of records in this PDB entry. ; _item.name '_database_PDB_rev_record.details' _item.category_id database_PDB_rev_record _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'Based on new data from author' 'For consistency with 1995-08-04 style-guide' 'For consistency with structural class' save_ save__database_PDB_rev_record.rev_num _item_description.description ; This data item is a pointer to _database_PDB_rev.num in the DATABASE_PDB_REV category. ; _item.name '_database_PDB_rev_record.rev_num' _item.mandatory_code yes save_ save__database_PDB_rev_record.type _item_description.description ; The types of records that were changed in this revision to a PDB entry. ; _item.name '_database_PDB_rev_record.type' _item.category_id database_PDB_rev_record _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'CRYST1' 'SCALE' 'MTRIX' 'ATOM' 'HETATM' save_ ######################## ## DATABASE_PDB_TVECT ## ######################## save_DATABASE_PDB_TVECT _category.description ; The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. ; _category.id database_pdb_tvect _category.mandatory_code no _category_key.name '_database_pdb_tvect.id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdb_group' save_ save__database_PDB_tvect.details _item_description.description ; A description of special aspects of this TVECT. ; _item.name '_database_PDB_tvect.details' _item.category_id database_PDB_tvect _item.mandatory_code no _item_type.code text save_ save__database_pdb_tvect.id _item_description.description ; The value of _database_PDB_tvect.id must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_database_pdb_tvect.id' _item.mandatory_code yes _item_type.code code save_ save__database_pdb_tvect.vector[1] _item_description.description ; The [1] element of the PDB TVECT vector. ; _item.name '_database_pdb_tvect.vector[1]' _item.category_id database_pdb_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_tvect.vector[2] _item_description.description ; The [2] element of the PDB TVECT vector. ; _item.name '_database_pdb_tvect.vector[2]' _item.category_id database_pdb_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ save__database_pdb_tvect.vector[3] _item_description.description ; The [3] element of the PDB TVECT vector. ; _item.name '_database_pdb_tvect.vector[3]' _item.category_id database_pdb_tvect _item.mandatory_code no _item_default.value 0.0 _item_sub_category.id vector _item_type.code float save_ ############ ## DIFFRN ## ############ save_DIFFRN _category.description ; Data items in the DIFFRN category record details about the diffraction data and its measurement. ; _category.id diffrn _category.mandatory_code no _category_key.name '_diffrn.id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn.id 'Set1' _diffrn.ambient_temp 293(3) _diffrn.ambient_environment ; Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air ; _diffrn.crystal_support ; 0.7 mm glass capillary, sealed with dental wax ; _diffrn.crystal_treatment ; Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection. ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn.id 'd1' _diffrn.details ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per min. Background counts for 5 sec on each side every scan. ; _diffrn.ambient_temp 293 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn.ambient_environment _item_description.description ; The gas or liquid surrounding the sample, if not air. ; _item.name '_diffrn.ambient_environment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_environment' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code line save_ save__diffrn.ambient_pressure _item_description.description ; The mean pressure in kilopascals at which the intensities were measured. ; _item.name '_diffrn.ambient_pressure' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_pressure' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_diffrn.ambient_pressure_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kilopascals save_ save__diffrn.ambient_pressure_esd _item_description.description ; The estimated standard deviation of _diffrn.ambient_pressure. ; _item.name '_diffrn.ambient_pressure_esd' _item.category_id diffrn _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_diffrn.ambient_pressure' _item_related.function_code associated_value _item_type.code float _item_units.code kilopascals save_ save__diffrn.ambient_temp _item_description.description ; The mean temperature in kelvins at which the intensities were measured. ; _item.name '_diffrn.ambient_temp' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_ambient_temperature' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_diffrn.ambient_temp_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code kelvin save_ save__diffrn.ambient_temp_details _item_description.description ; A description of special aspects of temperature control during data collection. ; _item.name '_diffrn.ambient_temp_details' _item.category_id diffrn _item.mandatory_code no _item_type.code text save_ save__diffrn.ambient_temp_esd _item_description.description ; The estimated standard deviation of _diffrn.ambient_temp. ; _item.name '_diffrn.ambient_temp_esd' _item.category_id diffrn _item.mandatory_code no _item_default.value 0.0 _item_related.related_name '_diffrn.ambient_temp' _item_related.function_code associated_value _item_type.code float _item_units.code kelvin save_ save__diffrn.crystal_id _item_description.description ; This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category. ; _item.name '_diffrn.crystal_id' _item.mandatory_code yes save_ save__diffrn.crystal_support _item_description.description ; The physical device used to support the crystal during data collection. ; _item.name '_diffrn.crystal_support' _item.category_id diffrn _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'glass capillary' 'quartz capillary' 'fiber' 'metal loop' save_ save__diffrn.crystal_treatment _item_description.description ; Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. ; _item.name '_diffrn.crystal_treatment' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_crystal_treatment' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case 'equilibrated in hutch for 24 hours' 'flash frozen in liquid nitrogen' 'slow cooled with direct air stream' save_ save__diffrn.details _item_description.description ; Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. ; _item.name '_diffrn.details' _item.category_id diffrn _item.mandatory_code no _item_aliases.alias_name '_diffrn_special_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ save__diffrn.id _item_description.description ; This data item uniquely identifies a set of diffraction data. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn.id' diffrn yes '_diffrn_detector.diffrn_id' diffrn_detector yes '_diffrn_measurement.diffrn_id' diffrn_measurement yes '_diffrn_orient_matrix.diffrn_id' diffrn_orient_matrix yes '_diffrn_orient_refln.diffrn_id' diffrn_orient_refln yes '_diffrn_radiation.diffrn_id' diffrn_radiation yes '_diffrn_refln.diffrn_id' diffrn_refln yes '_diffrn_reflns.diffrn_id' diffrn_reflns yes '_diffrn_source.diffrn_id' diffrn_source yes '_diffrn_standard_refln.diffrn_id' diffrn_standard_refln yes '_diffrn_standards.diffrn_id' diffrn_standards yes loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_detector.diffrn_id' '_diffrn.id' '_diffrn_measurement.diffrn_id' '_diffrn.id' '_diffrn_orient_matrix.diffrn_id' '_diffrn.id' '_diffrn_orient_refln.diffrn_id' '_diffrn.id' '_diffrn_radiation.diffrn_id' '_diffrn.id' '_diffrn_refln.diffrn_id' '_diffrn.id' '_diffrn_reflns.diffrn_id' '_diffrn.id' '_diffrn_source.diffrn_id' '_diffrn.id' '_diffrn_standard_refln.diffrn_id' '_diffrn.id' '_diffrn_standards.diffrn_id' '_diffrn.id' _item_type.code code save_ ####################### ## DIFFRN_ATTENUATOR ## ####################### save_DIFFRN_ATTENUATOR _category.description ; Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. ; _category.id diffrn_attenuator _category.mandatory_code no _category_key.name '_diffrn_attenuator.code' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_attenuator.code 1 _diffrn_attenuator.scale 16.976 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_attenuator.code _item_description.description ; A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln.attenuator_code which is stored with the diffraction data. See _diffrn_attenuator.scale. ; loop_ _item.name _item.category_id _item.mandatory_code '_diffrn_attenuator.code' diffrn_attenuator yes _item_aliases.alias_name '_diffrn_attenuator_code' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_linked.child_name _item_linked.parent_name '_diffrn_refln.attenuator_code' '_diffrn_attenuator.code' _item_type.code code save_ save__diffrn_attenuator.scale _item_description.description ; The scale factor applied when an intensity measurement is reduced by an attenuator identified by _diffrn_attenuator_code. This scale must be multiplied by the measured intensity to convert it to the same scale as unattenuated intensities. ; _item.name '_diffrn_attenuator.scale' _item.category_id diffrn_attenuator _item.mandatory_code no _item_aliases.alias_name '_diffrn_attenuator_scale' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ ##################### ## DIFFRN_DETECTOR ## ##################### save_DIFFRN_DETECTOR _category.description ; Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. ; _category.id diffrn_detector _category.mandatory_code no _category_key.name '_diffrn_detector.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn_detector.diffrn_id 'd1' _diffrn_detector.detector_type 'multiwire' _diffrn_detector.detector_specific 'Siemens' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_detector.details _item_description.description ; A description of special aspects of the radiation detector. ; _item.name '_diffrn_detector.details' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; Need new example here. ; save_ save__diffrn_detector.detector _item_description.description ; The general class of the radiation detector. ; _item.name '_diffrn_detector.detector' _item.category_id diffrn_detector _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_detector' cifdic.c91 1.0 '_diffrn_detector' cifdic.c94 2.0 _item_type.code text loop_ _item_examples.case 'photographic film' 'scintillation counter' 'CCD plate' 'BF~3~ counter' save_ save__diffrn_detector.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_detector.diffrn_id' _item.mandatory_code yes save_ save__diffrn_detector.dtime _item_description.description ; The deadtime in microseconds of the detectors used to measure the diffraction intensities. ; _item.name '_diffrn_detector.dtime' _item.category_id diffrn_detector _item.mandatory_code no loop_ _item_aliases.alias_name _item_aliases.dictionary _item_aliases.version '_diffrn_radiation_detector_dtime' cifdic.c91 1.0 '_diffrn_detector_dtime' cifdic.c94 2.0 loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_type.code float _item_units.code microseconds save_ save__diffrn_detector.type _item_description.description ; The make, model or name of the detector device used. ; _item.name '_diffrn_detector.type' _item.category_id diffrn_detector _item.mandatory_code no _item_aliases.alias_name '_diffrn_detector_type' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text save_ ######################## ## DIFFRN_MEASUREMENT ## ######################## save_DIFFRN_MEASUREMENT _category.description ; Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. ; _category.id diffrn_measurement _category.mandatory_code no _category_key.name '_diffrn_measurement.diffrn_id' loop_ _category_group.id 'inclusive_group' 'diffrn_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP ; ; _diffrn_measurement.diffrn_id 'd1' _diffrn_measurement.device_type '3-circle camera' _diffrn_measurement.device_specific 'Supper model x' _diffrn_measurement.device_details 'none' _diffrn_measurement.method 'omega scan' _diffrn_measurement.details ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. ; ; _diffrn_measurement.diffrn_id 's1' _diffrn_measurement.device 'Philips PW1100/20 diffractometer' _diffrn_measurement.method \q/2\q ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__diffrn_measurement.diffrn_id _item_description.description ; This data item is a pointer to _diffrn.id in the DIFFRN category. ; _item.name '_diffrn_measurement.diffrn_id' _item.mandatory_code yes save_ save__diffrn_measurement.details _item_description.description ; A description of special aspects of the intensity measurement. ; _item.name '_diffrn_measurement.details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees ; save_ save__diffrn_measurement.device _item_description.description ; The general class of goniometer or device used to support and orient the specimen. ; _item.name '_diffrn_measurement.device' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text loop_ _item_examples.case '3-circle camera' '4-circle camera' 'kappa-geometry camera' 'oscillation camera' 'precession camera' save_ save__diffrn_measurement.device_details _item_description.description ; A description of special aspects of the device used to measure the diffraction intensities. ; _item.name '_diffrn_measurement.device_details' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_details' _item_aliases.dictionary cifdic.c94 _item_aliases.version 2.0 _item_type.code text _item_examples.case ; Need new example here. ; save_ save__diffrn_measurement.device_type _item_description.description ; The make, model or name of the measurement device (goniometer) used. ; _item.name '_diffrn_measurement.device_type' _item.category_id diffrn_measurement _item.mandatory_code no _item_aliases.alias_name '_diffrn_measurement_device_type'